Define the function $\mathcal{I}:\mathbb{R}_{>0}^{2}\rightarrow\mathbb{R}$ via the definite integral
$$\mathcal{I}{\left(p,q\right)}:=\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\sqrt{t^{2}+p^{2}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}.\tag{1}$$
We seek a closed-form expression for $\mathcal{I}{\left(p,q\right)}$ for $\left(p,q\right)\in\mathbb{R}_{>0}^{2}$ such that $p>q$. It should be clear this problem is completely equivalent to the one posed by the OP.
We will make use of the following Euler substitution:
$$\sqrt{t^{2}+p^{2}}=t+x;~~~\small{p>0\land t\in\mathbb{R}\land x\in\mathbb{R}_{>0}}.\tag{2}$$
Solving for $t$, we have
$$t=\frac{p^{2}-x^{2}}{2x},$$
$$\implies\sqrt{t^{2}+p^{2}}=t+x=\frac{p^{2}+x^{2}}{2x},$$
$$\implies dt=dx\,\frac{(-1)\left(p^{2}+x^{2}\right)}{2x^{2}}.$$
Suppose $\left(p,q\right)\in\mathbb{R}_{>0}^{2}\land p>q$. We find
$$\begin{align}
\mathcal{I}{\left(p,q\right)}
&=\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\sqrt{t^{2}+p^{2}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\int_{0}^{1}\mathrm{d}t\,\frac{\left[\frac{\pi}{2}-\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}\right]}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\frac{\pi}{2}\int_{0}^{1}\mathrm{d}t\,\frac{1}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}-\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\frac{\pi}{2}\int_{0}^{\frac{1}{\sqrt{1+p^{2}}}}\mathrm{d}u\,\frac{1}{\left(1-u^{2}\right)}\cdot\frac{1}{\left(\frac{pu}{\sqrt{1-u^{2}}}\right)^{2}+q^{2}};~~~\small{\left[t=\frac{pu}{\sqrt{1-u^{2}}}\right]}\\
&~~~~~-\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\frac{\pi}{2}\int_{0}^{\frac{1}{\sqrt{1+p^{2}}}}\mathrm{d}u\,\frac{1}{p^{2}u^{2}+q^{2}\left(1-u^{2}\right)}-\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\frac{\pi}{2}\int_{0}^{\frac{1}{\sqrt{1+p^{2}}}}\mathrm{d}u\,\frac{1}{q^{2}+\left(p^{2}-q^{2}\right)u^{2}}-\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\frac{\pi}{2}\int_{0}^{\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}}\mathrm{d}v\,\frac{q}{\sqrt{p^{2}-q^{2}}}\cdot\frac{1}{q^{2}+q^{2}v^{2}};~~~\small{\left[u=\frac{qv}{\sqrt{p^{2}-q^{2}}}\right]}\\
&~~~~~-\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\frac{\pi}{2}\cdot\frac{1}{q\sqrt{p^{2}-q^{2}}}\int_{0}^{\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}}\mathrm{d}v\,\frac{1}{1+v^{2}}-\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}.\tag{3a}\\
\end{align}$$
Then $0<-1+\sqrt{1+p^{2}}<p$, and
$$\begin{align}
\mathcal{I}{\left(p,q\right)}
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\int_{0}^{1}\mathrm{d}t\,\frac{\arctan{\left(\frac{1}{\sqrt{t^{2}+p^{2}}}\right)}}{\left(t^{2}+q^{2}\right)\sqrt{t^{2}+p^{2}}}\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}\\
&~~~~~-\int_{p}^{-1+\sqrt{1+p^{2}}}\mathrm{d}x\,\frac{(-1)\left(p^{2}+x^{2}\right)}{2x^{2}}\cdot\frac{1}{\left(\frac{p^{2}-x^{2}}{2x}\right)^{2}+q^{2}}\cdot\frac{2x}{p^{2}+x^{2}}\\
&~~~~~\times\arctan{\left(\frac{2x}{p^{2}+x^{2}}\right)};~~~\small{\left[-t+\sqrt{t^{2}+p^{2}}=x\right]}\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\int_{-1+\sqrt{1+p^{2}}}^{p}\mathrm{d}x\,\frac{4x\arctan{\left(\frac{2x}{p^{2}+x^{2}}\right)}}{\left(p^{2}-x^{2}\right)^{2}+4q^{2}x^{2}}.\tag{3b}\\
\end{align}$$
It follows from the arctangent addition formula that
$$\arctan{\left(\frac{x}{-1+\sqrt{1+p^{2}}}\right)}-\arctan{\left(\frac{x}{1+\sqrt{1+p^{2}}}\right)}=\arctan{\left(\frac{2x}{p^{2}+x^{2}}\right)};~~~\small{p\in\mathbb{R}_{>0}\land x\in\mathbb{R}}.\tag{4}$$
Set $r:=\frac{p}{1+\sqrt{1+p^{2}}}\land\sigma:=\arcsin{\left(\frac{q}{p}\right)}$. Then, $0<r<1\land0<\sigma<\frac{\pi}{2}\land r^{-1}=\frac{1+\sqrt{1+p^{2}}}{p}=\frac{p}{-1+\sqrt{1+p^{2}}}$, and
$$\begin{align}
\mathcal{I}{\left(p,q\right)}
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\int_{-1+\sqrt{1+p^{2}}}^{p}\mathrm{d}x\,\frac{4x\arctan{\left(\frac{2x}{p^{2}+x^{2}}\right)}}{\left(p^{2}-x^{2}\right)^{2}+4q^{2}x^{2}}\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\int_{-1+\sqrt{1+p^{2}}}^{p}\mathrm{d}x\,\frac{4x}{\left(p^{2}-x^{2}\right)^{2}+4q^{2}x^{2}}\\
&~~~~~\times\left[\arctan{\left(\frac{x}{-1+\sqrt{1+p^{2}}}\right)}-\arctan{\left(\frac{x}{1+\sqrt{1+p^{2}}}\right)}\right]\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\int_{\frac{-1+\sqrt{1+p^{2}}}{p}}^{1}\mathrm{d}y\,\frac{4p^{2}y}{\left(p^{2}-p^{2}y^{2}\right)^{2}+4p^{2}q^{2}y^{2}}\\
&~~~~~\times\left[\arctan{\left(\frac{py}{-1+\sqrt{1+p^{2}}}\right)}-\arctan{\left(\frac{py}{1+\sqrt{1+p^{2}}}\right)}\right];~~~\small{\left[x=py\right]}\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\frac{1}{p^{2}}\int_{\frac{-1+\sqrt{1+p^{2}}}{p}}^{1}\mathrm{d}y\,\frac{4y}{\left(1-y^{2}\right)^{2}+4\left(\frac{q}{p}\right)^{2}y^{2}}\\
&~~~~~\times\left[\arctan{\left(\frac{py}{-1+\sqrt{1+p^{2}}}\right)}-\arctan{\left(\frac{py}{1+\sqrt{1+p^{2}}}\right)}\right]\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\frac{1}{p^{2}}\int_{r}^{1}\mathrm{d}y\,\frac{4y}{\left(1-y^{2}\right)^{2}+4y^{2}\sin^{2}{\left(\sigma\right)}}\\
&~~~~~\times\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right]\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\frac{1}{p^{2}}\int_{r}^{1}\mathrm{d}y\,\frac{4y\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right]}{1-2y^{2}\left[1-2\sin^{2}{\left(\sigma\right)}\right]+y^{4}}\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}-\frac{1}{p^{2}}\int_{r}^{1}\mathrm{d}y\,\frac{4y\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right]}{1-2y^{2}\cos{\left(2\sigma\right)}+y^{4}}\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}\\
&~~~~~-\frac{1}{p^{2}}\int_{r}^{1}\mathrm{d}y\,\frac{4y\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right]}{\left[1-2y\cos{\left(\sigma\right)}+y^{2}\right]\left[1+2y\cos{\left(\sigma\right)}+y^{2}\right]}\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}\\
&~~~~~-\frac{1}{p^{2}\cos{\left(\sigma\right)}}\int_{r}^{1}\mathrm{d}y\,\frac{4y\cos{\left(\sigma\right)}}{\left[1-2y\cos{\left(\sigma\right)}+y^{2}\right]\left[1+2y\cos{\left(\sigma\right)}+y^{2}\right]}\\
&~~~~~\times\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right]\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}\\
&~~~~~-\frac{1}{p^{2}\cos{\left(\sigma\right)}}\int_{r}^{1}\mathrm{d}y\,\left[\frac{1}{1-2y\cos{\left(\sigma\right)}+y^{2}}-\frac{1}{1+2y\cos{\left(\sigma\right)}+y^{2}}\right]\\
&~~~~~\times\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right]\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}\\
&~~~~~-\frac{1}{p^{2}\sin{\left(\sigma\right)}\cos{\left(\sigma\right)}}\int_{r}^{1}\mathrm{d}y\,\left[\frac{\sin{\left(\sigma\right)}}{1-2y\cos{\left(\sigma\right)}+y^{2}}-\frac{\sin{\left(\sigma\right)}}{1+2y\cos{\left(\sigma\right)}+y^{2}}\right]\\
&~~~~~\times\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right]\\
&=\frac{\pi\arctan{\left(\frac{\sqrt{p^{2}-q^{2}}}{q\sqrt{1+p^{2}}}\right)}}{2q\sqrt{p^{2}-q^{2}}}\\
&~~~~~-\frac{1}{q\sqrt{p^{2}-q^{2}}}\int_{r}^{1}\mathrm{d}y\,\left[\frac{\sin{\left(\sigma\right)}}{1-2y\cos{\left(\sigma\right)}+y^{2}}-\frac{\sin{\left(\sigma\right)}}{1+2y\cos{\left(\sigma\right)}+y^{2}}\right]\\
&~~~~~\times\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right].\tag{5}\\
\end{align}$$
As such, let's introduce another auxiliary function $\mathcal{J}:\left(0,1\right)\times\left(0,\frac{\pi}{2}\right)\rightarrow\mathbb{R}$ defined via the last definite integral above:
$$\mathcal{J}{\left(r,\sigma\right)}:=\int_{r}^{1}\mathrm{d}y\,\left[\frac{\sin{\left(\sigma\right)}}{1-2y\cos{\left(\sigma\right)}+y^{2}}-\frac{\sin{\left(\sigma\right)}}{1+2y\cos{\left(\sigma\right)}+y^{2}}\right]\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right].\tag{6}$$
Given $\left(r,\sigma\right)\in\left(0,1\right)\times\left(0,\frac{\pi}{2}\right)$, we find
$$\begin{align}
\mathcal{J}{\left(r,\sigma\right)}
&=\int_{r}^{1}\mathrm{d}y\,\left[\frac{\sin{\left(\sigma\right)}}{1-2y\cos{\left(\sigma\right)}+y^{2}}-\frac{\sin{\left(\sigma\right)}}{1+2y\cos{\left(\sigma\right)}+y^{2}}\right]\\
&~~~~~\times\left[\arctan{\left(\frac{y}{r}\right)}-\arctan{\left(ry\right)}\right]\\
&=\int_{r}^{1}\mathrm{d}y\,\left[\frac{\sin{\left(\sigma\right)}}{1-2y\cos{\left(\sigma\right)}+y^{2}}-\frac{\sin{\left(\sigma\right)}}{1+2y\cos{\left(\sigma\right)}+y^{2}}\right]\arctan{\left(\frac{y}{r}\right)}\\
&~~~~~-\int_{r}^{1}\mathrm{d}y\,\left[\frac{\sin{\left(\sigma\right)}}{1-2y\cos{\left(\sigma\right)}+y^{2}}-\frac{\sin{\left(\sigma\right)}}{1+2y\cos{\left(\sigma\right)}+y^{2}}\right]\arctan{\left(ry\right)}\\
&=\int_{1}^{\frac{1}{r}}\mathrm{d}t\,\left[\frac{r\sin{\left(\sigma\right)}}{1-2rt\cos{\left(\sigma\right)}+r^{2}t^{2}}-\frac{r\sin{\left(\sigma\right)}}{1+2rt\cos{\left(\sigma\right)}+r^{2}t^{2}}\right]\arctan{\left(t\right)};~~~\small{\left[y=rt\right]}\\
&~~~~~-\int_{r^{2}}^{r}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\arctan{\left(u\right)};~~~\small{\left[y=\frac{u}{r}\right]}\\
&=\int_{r}^{1}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\\
&~~~~~\times\arctan{\left(\frac{1}{u}\right)};~~~\small{\left[t=u^{-1}\right]}\\
&~~~~~-\int_{r^{2}}^{r}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\arctan{\left(u\right)}\\
&=\int_{r}^{1}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\left[\frac{\pi}{2}-\arctan{\left(u\right)}\right]\\
&~~~~~-\int_{r^{2}}^{r}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\arctan{\left(u\right)}\\
&=\frac{\pi}{2}\int_{r}^{1}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\\
&~~~~~-\int_{r}^{1}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\arctan{\left(u\right)}\\
&~~~~~-\int_{r^{2}}^{r}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\arctan{\left(u\right)}\\
&=\frac{\pi}{2}\int_{r}^{1}\mathrm{d}u\,\frac{d}{du}\left[\arctan{\left(\frac{u-r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}-\arctan{\left(\frac{u+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}\right]\\
&~~~~~-\int_{r^{2}}^{1}\mathrm{d}u\,\left[\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}-\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\right]\arctan{\left(u\right)}\\
&=\frac{\pi}{2}\bigg{[}\arctan{\left(\frac{1-r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}-\arctan{\left(\frac{1+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}\\
&~~~~~-\arctan{\left(\frac{1-\cos{\left(\sigma\right)}}{\sin{\left(\sigma\right)}}\right)}+\arctan{\left(\frac{1+\cos{\left(\sigma\right)}}{\sin{\left(\sigma\right)}}\right)}\bigg{]}\\
&~~~~~+\int_{r^{2}}^{1}\mathrm{d}u\,\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\arctan{\left(u\right)}\\
&~~~~~-\int_{r^{2}}^{1}\mathrm{d}u\,\frac{r\sin{\left(\sigma\right)}}{r^{2}-2ru\cos{\left(\sigma\right)}+u^{2}}\arctan{\left(u\right)}\\
&=\frac{\pi}{2}\left[\frac{\pi}{2}-\sigma-\arctan{\left(\frac{r^{2}\sin{\left(2\sigma\right)}}{1-r^{2}\cos{\left(2\sigma\right)}}\right)}\right]\\
&~~~~~+\int_{r^{2}}^{1}\mathrm{d}u\,\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\arctan{\left(u\right)}\\
&~~~~~+\int_{-1}^{-r^{2}}\mathrm{d}u\,\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\arctan{\left(u\right)};~~~\small{\left[u\mapsto-u\right]}\\
&=\frac{\pi}{2}\left[\frac{\pi}{2}-\sigma-\arctan{\left(\frac{r^{2}\sin{\left(2\sigma\right)}}{1-r^{2}\cos{\left(2\sigma\right)}}\right)}\right]\\
&~~~~~+\int_{-1}^{1}\mathrm{d}u\,\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\arctan{\left(u\right)}\\
&~~~~~-\int_{-r^{2}}^{r^{2}}\mathrm{d}u\,\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\arctan{\left(u\right)}.\tag{7}\\
\end{align}$$
To facilitate the evaluation of the remaining two integrals in the last line above, we introduce yet another auxiliary function $\mathcal{K}:\left(0,1\right)\times\left(0,\frac{\pi}{2}\right)\times\left(0,1\right]\rightarrow\mathbb{R}$ defined via the definite integral
$$\mathcal{K}{\left(r,\sigma,z\right)}:=\int_{-z}^{z}\mathrm{d}u\,\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\arctan{\left(u\right)}.\tag{8}$$
Suppose $\left(r,\sigma,z\right)\in\left(0,1\right)\times\left(0,\frac{\pi}{2}\right)\times\left(0,1\right]$. We then have
$$\begin{align}
\mathcal{K}{\left(r,\sigma,z\right)}
&=\int_{-z}^{z}\mathrm{d}u\,\frac{r\sin{\left(\sigma\right)}}{r^{2}+2ru\cos{\left(\sigma\right)}+u^{2}}\arctan{\left(u\right)}\\
&=\int_{-z}^{z}\mathrm{d}u\,\arctan{\left(u\right)}\frac{d}{du}\arctan{\left(\frac{u+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}\\
&=\arctan{\left(z\right)}\arctan{\left(\frac{z+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}-\arctan{\left(-z\right)}\arctan{\left(\frac{-z+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}\\
&~~~~~-\int_{-z}^{z}\mathrm{d}u\,\arctan{\left(\frac{u+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}\frac{d}{du}\arctan{\left(u\right)};~~~\small{I.B.P.}\\
&=\arctan{\left(z\right)}\arctan{\left(\frac{z+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}-\arctan{\left(z\right)}\arctan{\left(\frac{z-r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}\\
&~~~~~-\int_{-z}^{z}\mathrm{d}u\,\frac{1}{1+u^{2}}\arctan{\left(\frac{r\cos{\left(\sigma\right)}+u}{r\sin{\left(\sigma\right)}}\right)}\\
&=\arctan{\left(z\right)}\left[\arctan{\left(\frac{z+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}-\arctan{\left(\frac{z-r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}\right]\\
&~~~~~-\int_{-z}^{z}\mathrm{d}u\,\frac{1}{1+u^{2}}\arctan{\left(\cot{\left(\sigma\right)}+r^{-1}u\csc{\left(\sigma\right)}\right)}\\
&=\arctan{\left(z\right)}\left[\arctan{\left(\frac{z+r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}-\arctan{\left(\frac{z-r\cos{\left(\sigma\right)}}{r\sin{\left(\sigma\right)}}\right)}\right]\\
&~~~~~-\int_{-\arctan{\left(z\right)}}^{\arctan{\left(z\right)}}\mathrm{d}\varphi\,\arctan{\left(\cot{\left(\sigma\right)}+r^{-1}\csc{\left(\sigma\right)}\tan{\left(\varphi\right)}\right)};~~~\small{\left[\arctan{\left(u\right)}=\varphi\right]}.\tag{9}\\
\end{align}$$
Suppose $\left(a,b,\psi,\omega\right)\in\mathbb{R}\times\mathbb{R}\times\left(-\frac{\pi}{2},\frac{\pi}{2}\right)\times\left(-\frac{\pi}{2},\frac{\pi}{2}\right)$, and assume
$$0<a\land\sqrt{1+a^{2}}<b\land-\frac{\pi}{4}\le\psi<\omega\le\frac{\pi}{4}.$$
Set
$$B:=\frac{\left[\sqrt{a^{2}+\left(b+1\right)^{2}}+\sqrt{a^{2}+\left(b-1\right)^{2}}\right]^{2}}{4b}\land\phi:=\frac12\arctan{\left(\frac{2ab}{b^{2}-a^{2}-1}\right)},$$
and note that $1<B\land0<\phi<\frac{\pi}{4}$. Then, it can be shown that
$$\begin{align}
\int_{\psi}^{\omega}\mathrm{d}\varphi\,\arctan{\left(a+b\tan{\left(\varphi\right)}\right)}
&=\frac12\left(\phi+\omega\right)^{2}-\frac12\left(\phi+\psi\right)^{2}\\
&~~~~~-\left(\omega-\psi\right)\arctan{\left(\frac{\tan{\left(\phi\right)}}{B}\right)}\\
&~~~~~-\frac12\operatorname{Li}_{2}{\left(\frac{1-B}{1+B},\pi-2\phi-2\omega\right)}\\
&~~~~~+\frac12\operatorname{Li}_{2}{\left(\frac{1-B}{1+B},\pi-2\phi-2\psi\right)}.\tag{10}\\
\end{align}$$
The integration formula above is derived in this question.
Integration formula $(10)$ is sufficient to provide us with a closed-form expression for $\mathcal{K}$, and in turn $\mathcal{J}$ and $\mathcal{I}$ as well. So our work is complete in principle, and all that remains is to substitute back the chain of results to obtain a final expression in terms of the original variables. (Forgive me if I don't bother to do that here since the end result is such a cumbersome expression.)