Without loss of generality we can assume that $\Sigma$ is a diagonal matrix. Indeed since $\Sigma$ is a full rank symmetric matrix it has a spectral decomposition $\Sigma = O^T \cdot {\mathcal D} \cdot O$ where $O\cdot O^T = O^T\cdot O=1$ and ${\mathcal D}:=(s_1,s_2,s_3)$ is diagonal. Then of course $\Sigma^{-1} = O^T \cdot {\mathcal D}^{-1} \cdot O$ and
\begin{equation}
Tr\left( \Sigma^{-1} \cdot H L H^T \right)=
Tr\left( O^T \cdot {\mathcal D}^{-1} \cdot O \cdot H L H^T\right) =
Tr\left( {\mathcal D}^{-1} O \cdot H L H^T O^T\right)=
Tr\left({\mathcal D}^{-1} \cdot OH \cdot L \cdot (OH)^T\right)
\end{equation}
where we used the cyclic property of the trace. Now in our integral we can change variables $H \rightarrow OH$ and use the fact that the Jacobian of this mapping is unity.
Now we construct an orthogonal matrix as a product of three rotational matrices each one in three mutually orthogonal planes, $(1,2)$, $(1,3)$ and $(2,3)$ respectively. We have:
\begin{eqnarray}
&&\left(H_{1,2},H_{1,3},H_{2,3}\right) = \\&&
\left(
\left(\begin{array}{ccc} \cos(\phi_1) & -\sin(\phi_1) & 0 \\ \sin(\phi_1) & \cos(\phi_1) & 0 \\ 0 & 0 & 1 \end{array} \right),
\left(\begin{array}{ccc} \cos(\phi_2) & 0 & -\sin(\phi_2) \\ 0 & 1 & 0 \\ \sin(\phi_2) & 0 & \cos(\phi_2) \end{array} \right),
\left(\begin{array}{ccc} 1 & 0 & 0 \\ 0 & \cos(\phi_3) & -\sin(\phi_3) \\ 0 & \sin(\phi_3) & \cos(\phi_3) \end{array} \right)
\right)
\end{eqnarray}
Therefore:
\begin{eqnarray}
&&H= H_{1,2} H_{1,3} H_{2,3} = \\ &&
\begin{array}{rrr}
\cos(\phi_1) \cos(\phi_2),& -\cos(\phi_3) \sin(\phi_1) -
\cos(\phi_1) \sin(\phi_2) \sin(\phi_3),& -\cos(\phi_1) \cos(\phi_3) \sin(\phi_2) +
\sin(\phi_1) \sin(\phi_3) \\
\cos(\phi_2) \sin(\phi_1),&
\cos(\phi_1) \cos(\phi_3) -
\sin(\phi_1) \sin(\phi_2) \sin(\phi_3),& -\cos(\phi_3) \sin(\phi_1) \sin(\phi_2) -
\cos(\phi_1) \sin(\phi_3) \\
\sin(\phi_2),&\cos(\phi_2) \sin(\phi_3),&\cos(\phi_2) \cos(\phi_3)
\end{array}
\end{eqnarray}
The Jacobian of the mapping from the matrix elements to the eigenvalues and the angles is quite simple, much simpler than before. It reads:
\begin{equation}
\frac{\partial(c_{1,1},c_{2,2},c_{3,3},c_{1,2},c_{1,3},c_{2,3})}{\partial(l_1,l_2,l_3,\phi_1,\phi_2,\phi_3)} =
(l_1-l_2)(l_1-l_3)(l_2-l_3) \cos(\phi_2)
\end{equation}
where
\begin{equation}
\left(
\begin{array}{ccc} c_{1,1} & c_{2,2} & c_{1,3} \\ c_{1,2} & c_{2,2} & c_{2,3} \\ c_{1,3} & c_{2,3} & c_{3,3}
\end{array}
\right) = H L H^T
\end{equation}
The expression inside the exponential reads:
\begin{eqnarray}
&& Tr\left[\Sigma^{-1} H L H^T\right] =\\&&
\left(\sum\limits_{j=1}^3 {\mathcal A}_j l_j\right) +\\
&&
\sum\limits_{j=1}^3 {\mathcal X}_j \cdot \cos(2 \phi_j) +
\sum\limits_{1\le i < j \le 3} {\mathcal X}^+_{i,j} \cdot \cos(2\phi_i+2\phi_j) +
\sum\limits_{1\le i < j \le 3} {\mathcal X}^-_{i,j} \cdot \cos(2\phi_i-2\phi_j) +\\
&&\sum_{1\le i<j<k\le 3} {\mathcal X}_{i,j,k} \cos(2(\phi_i+\phi_j+\phi_k))+\\
&&\sum_{1\le i<j<k\le 3} {\mathcal X}^{(-,+,+)}_{i,j,k} \cos(2(-\phi_i+\phi_j+\phi_k))+\\
&&\sum_{1\le i<j<k\le 3} {\mathcal X}^{(+,-,+)}_{i,j,k} \cos(2(\phi_i-\phi_j+\phi_k))+\\
&&\sum_{1\le i<j<k\le 3} {\mathcal X}^{(+,+,-)}_{i,j,k} \cos(2(\phi_i+\phi_j-\phi_k))+\\
&&\sum\limits_{1\le i<j<k\le 3} {\mathcal Y}_{i,j,k} \sin(2 \phi_i+\phi_j+2 \phi_k)+\\
&&\sum\limits_{1\le i<j<k\le 3} {\mathcal Y}^{(-,+,+)}_{i,j,k} \sin(-2 \phi_i+\phi_j+2 \phi_k)+\\
&&\sum\limits_{1\le i<j<k\le 3} {\mathcal Y}^{(+,-,+)}_{i,j,k} \sin(2 \phi_i-\phi_j+2 \phi_k)+\\
&&\sum\limits_{1\le i<j<k\le 3} {\mathcal Y}^{(+,+,-)}_{i,j,k} \sin(2 \phi_i+\phi_j-2 \phi_k)
\end{eqnarray}
where
\begin{eqnarray}
{\mathcal A}_1 &=& \frac{1}{4 s_1}+\frac{1}{4 s_2}+\frac{1}{2 s_3} \\
{\mathcal A}_2 &=& \frac{3}{8 s_1}+\frac{3}{8 s_2}+\frac{1}{4 s_3} \\
{\mathcal A}_3 &=& \frac{3}{8 s_1}+\frac{3}{8 s_2}+\frac{1}{4 s_3}
\end{eqnarray}
and
\begin{equation}
\sum\limits_{j=1}^3 {\mathcal A}_j = \frac{1}{s_1}+\frac{1}{s_2}+\frac{1}{s_3} =
=
\frac{1}{2} \frac{\left(Tr[\Sigma]^2 - Tr[\Sigma^2]\right)}{\det(\Sigma)}
\end{equation}
and
\begin{eqnarray}
{\mathcal X}_1 &=& \frac{1}{8}((l_2-l_1)+(l_3-l_1)) \frac{s_1-s_2}{s_1 s_2}\\
{\mathcal X}_2 &=& \frac{1}{8}((l_2-l_1)+(l_3-l_1)) \left( \frac{s_2-s_3}{s_2 s_3} + \frac{s_1-s_3}{s_1 s_3}\right) \\
{\mathcal X}_3 &=& \frac{1}{8} (l_3-l_2) \left( \frac{s_2-s_3}{s_2 s_3} + \frac{s_1-s_3}{s_1 s_3}\right)\\
{\mathcal X}^+_{1,2} &=&\frac{1}{16} ((l_2-l_1)+(l_3-l_1)) \frac{s_1-s_2}{s_1 s_2}\\
{\mathcal X}^+_{1,3} &=&\frac{3}{16} (l_2-l_3) \frac{s_1-s_2}{s_1 s_2}\\
{\mathcal X}^+_{2,3} &=& \frac{1}{16} (l_3-l_2) \left( \frac{s_2-s_3}{s_2 s_3} + \frac{s_1-s_3}{s_1 s_3}\right)\\
{\mathcal X}^-_{1,2} &=& {\mathcal X}^+_{1,2}\\
{\mathcal X}^-_{2,3} &=& {\mathcal X}^+_{2,3}\\
{\mathcal X}^-_{1,3} &=& {\mathcal X}^+_{1,3}\\
{\mathcal X}_{1,2,3}&=& \frac{1}{32} (l_3-l_2)\frac{s_1-s_2}{s_1 s_2}\\
{\mathcal X}^{(-,+,+)}_{1,2,3}&=&{\mathcal X}_{1,2,3}\\
{\mathcal X}^{(+,-,+)}_{1,2,3}&=&{\mathcal X}_{1,2,3}\\
{\mathcal X}^{(+,+,-)}_{1,2,3}&=&{\mathcal X}_{1,2,3}\\
{\mathcal Y}_{1,2,3}&=& \frac{1}{8} (l_2-l_3) \frac{s_1-s_2}{s_1 s_2}\\
{\mathcal Y}^{(-,+,+)}_{1,2,3}&=&-{\mathcal Y}_{1,2,3}\\
{\mathcal Y}^{(+,-,+)}_{1,2,3}&=&-{\mathcal Y}_{1,2,3}\\
{\mathcal Y}^{(+,+,-)}_{1,2,3}&=&-{\mathcal Y}_{1,2,3}
\end{eqnarray}
Therefore the final result has the same form as before:
\begin{eqnarray}
&&I = \Delta(\vec{l}) \cdot e^{-\frac{1}{2} \sum\limits_{j=1}^3 {\mathcal A}_j l_j} \cdot
\int\limits_{[0,2\pi]^3} \left|\cos(\phi_2)\right| \\&&
\exp(-1/2)\left(\right.\\
&&\sum\limits_{j=1}^3 {\mathcal X}_j \cdot \cos(2 \phi_j) +
\sum\limits_{1\le i < j \le 3} {\mathcal X}^+_{i,j} \cdot \cos(2\phi_i+2\phi_j) +
\sum\limits_{1\le i < j \le 3} {\mathcal X}^-_{i,j} \cdot \cos(2\phi_i-2\phi_j) +\\
&&\sum_{1\le i<j<k\le 3} {\mathcal X}_{i,j,k} \cos(2(\phi_i+\phi_j+\phi_k))+\\
&&\sum_{1\le i<j<k\le 3} {\mathcal X}^{(-,+,+)}_{i,j,k} \cos(2(-\phi_i+\phi_j+\phi_k))+\\
&&\sum_{1\le i<j<k\le 3} {\mathcal X}^{(+,-,+)}_{i,j,k} \cos(2(\phi_i-\phi_j+\phi_k))+\\
&&\sum_{1\le i<j<k\le 3} {\mathcal X}^{(+,+,-)}_{i,j,k} \cos(2(\phi_i+\phi_j-\phi_k))+\\
&&\sum\limits_{1\le i<j<k\le 3} {\mathcal Y}_{i,j,k} \sin(2 \phi_i+\phi_j+2 \phi_k)+\\
&&\sum\limits_{1\le i<j<k\le 3} {\mathcal Y}^{(-,+,+)}_{i,j,k} \sin(-2 \phi_i+\phi_j+2 \phi_k)+\\
&&\sum\limits_{1\le i<j<k\le 3} {\mathcal Y}^{(+,-,+)}_{i,j,k} \sin(2 \phi_i-\phi_j+2 \phi_k)+\\
&&\sum\limits_{1\le i<j<k\le 3} {\mathcal Y}^{(+,+,-)}_{i,j,k} \sin(2 \phi_i+\phi_j-2 \phi_k)\\
&&\left.
\right)
\prod\limits_{j=1}^3 d\phi_j \quad (ii)
\end{eqnarray}
This integral defines a Generalized (matrix) Bessel function (see
Dattoli, G.; Torre, A.; Lorenzutta, S., Theory of multivariable Bessel functions and elliptic modular functions, Matematiche 53, No. 2, 387-399 (1998). ZBL1156.33303. for example) and therefore can be expressed as follows:
\begin{eqnarray}
&&I = \Delta(\vec{l}) \cdot e^{-\frac{1}{2} \sum\limits_{j=1}^3 {\mathcal A}_j l_j} \cdot \underline{(2\pi)^2 \cdot \frac{4 (-1)^{|{\mathcal N}|/2+1}}{{\mathcal N}^2-1} }\cdot \left\{ \right.\\
&&
\prod\limits_{j=1}^3 \left[\imath ^{n_j} \cdot J_{n_j}\left(\frac{\imath}{2} {\mathcal X}_j\right)\right] \cdot
\prod\limits_{\begin{array}{c} 1 \le i < j \le 3 \\ \xi=\pm \end{array} }
\left[
\imath^{n^{(\xi)}_{i,j}} \cdot J_{n^{(\xi)}_{i,j}}\left(\frac{\imath}{2} {\mathcal X}^{\xi}_{i,j} \right)
\right] \cdot \\
&&
\prod\limits_{\xi=0}^3 \left[
\imath^{n^{c,\vec{e}_\xi}} \cdot J_{n^{c,\vec{e}_\xi}}\left( \frac{\imath}{2} {\mathcal X}_{1,2,3}^{\vec{e}_\xi}\right)
\right] \cdot
\prod\limits_{\xi=0}^3 \left[
J_{n^{s,\vec{e}_\xi}} \left( \frac{\imath}{2} {\mathcal Y}_{1,2,3}^{\vec{e}_\xi}\right)
\right] \\
\left. \right\} \quad (ii)
\end{eqnarray}
where the quantity in curly braces in the right hand side is being summed over $ \vec{n}:= \left(n_1,n_2,n_3;n_{1,2}^{+},n_{1,2}^{-},n_{1,3}^{+},n_{1,3}^{-},n_{2,3}^{+},n_{2,3}^{-};(n^{c,\vec{e}_\xi})_{\xi=0}^3; (n^{s,\vec{e}_\xi})_{\xi=0}^3 \right) \in {\mathbb Z}^{17} $ subject to following constraints:
\begin{eqnarray}
2 n_1 &+&
2(\begin{array}{c} n_{1,2}^{+}+n_{1,2}^{-}\\
+ n_{1,3}^{+}+n_{1,3}^{-} \end{array}) +
2(\begin{array}{c} n^{c,\vec{e}_0}-n^{c,\vec{e}_1} \\ +n^{c,\vec{e}_2} + n^{c,\vec{e}_3} \end{array}) +
2(\begin{array}{c} n^{s,\vec{e}_0}-n^{s,\vec{e}_1} \\ +n^{s,\vec{e}_2} + n^{s,\vec{e}_3} \end{array}) &=& 0 \\
%
2 n_2 &+&
2(\begin{array}{c} n_{1,2}^{+}-n_{1,2}^{-}\\
+ n_{2,3}^{+}+n_{2,3}^{-} \end{array}) +
2(\begin{array}{c} n^{c,\vec{e}_0}+n^{c,\vec{e}_1} \\ -n^{c,\vec{e}_2} + n^{c,\vec{e}_3} \end{array}) +
1(\begin{array}{c} n^{s,\vec{e}_0}+n^{s,\vec{e}_1} \\ -n^{s,\vec{e}_2} + n^{s,\vec{e}_3} \end{array}) &=& {\mathcal N} \in 2{\mathbb N} \\
%
2 n_3 &+&
2(\begin{array}{c} n_{1,3}^{+}-n_{1,3}^{-}\\
+ n_{2,3}^{+}-n_{2,3}^{-} \end{array}) +
2(\begin{array}{c} n^{c,\vec{e}_0}+n^{c,\vec{e}_1} \\ +n^{c,\vec{e}_2} - n^{c,\vec{e}_3} \end{array}) +
2(\begin{array}{c} n^{s,\vec{e}_0}+n^{s,\vec{e}_1} \\ +n^{s,\vec{e}_2} - n^{s,\vec{e}_3} \end{array}) &=& 0
\end{eqnarray}
In here $ \left( \vec{e}_\xi \right)_{\xi=0}^3 $ are defined as follows:
\begin{eqnarray}
\vec{e}_0 &=& (+,+,+) \\
\vec{e}_1 &=& (-,+,+) \\
\vec{e}_2 &=& (+,-,+) \\
\vec{e}_3 &=& (+,+,-)
\end{eqnarray}
Note 0: Equation $(ii) $ follows from applying the Jacobi-Anger expansion to each of the seventeen terms inside the exponential in $(i)$ and then using the orthogonality of plane waves along with the following identity:
\begin{equation}
\int\limits_0^{2\pi} e^{\imath n \phi} \cdot \left| \cos(\phi) \right| d\phi =
\left\{
\begin{array}{lll}
\frac{4 (-1)^{|n|/2+1} }{n^2-1} & \quad \mbox{if $n$ is even }\\
0 & \quad \mbox{otherwise}
\end{array}
\right.
\end{equation}
Note 1: In general the integral over the angles, ie.e equation $(ii)$, depends only on $\left(l_1-l_2, l_1-l_3, l_2-l_3\right)$ on one hand and on $\left(1/s_1-1/s_2, 1/s_1-1/s_3, 1/s_2-1/s_3\right)$ on the other hand.
Note 2: On the face of it equation $(ii)$ does not seem to be useful in the generic case, since it is not quite clear how fast that multiple sum will converge, however in some particular cases that equation might be useful. Let us list some of those cases now.
- Take $s_1=s_2=s_3= s$. Then $\vec{n} = \left(\underbrace{0,\cdots,0}_{17}\right)$ and ${\mathcal N}= 0$ and $I = \Delta(\vec{l}) \cdot e^{-1/(2 s) \cdot Tr[L]} \cdot (2\pi)^2 \cdot 4 $. This makes sense by comparing with the definition in the body of the question.
- Take $s_1=s_2 \neq s_3$. Then $\vec{n} = \left(0,n_2,n_3;0,0,0,0,n_{2,3}^+,n_{2,3}^{-};(0)_{\xi=0}^3;(0)_{\xi=0}^3 \right)$. Then the result reads:
\begin{eqnarray}
&&I = \Delta(\vec{l}) \cdot e^{-\frac{1}{2} \sum\limits_{j=1}^3 {\mathcal A}_j l_j} \cdot \underline{(2\pi)^2 \cdot \frac{4 (-1)^{|{\mathcal N}|/2+1}}{{\mathcal N}^2-1} }\cdot \left\{ \right.\\
&&
\prod\limits_{j=2}^3 \left[\imath ^{n_j} \cdot J_{n_j}\left(\frac{\imath}{2} {\mathcal X}_j\right)\right] \cdot
\prod\limits_{\begin{array}{c} (i,j)=(2,3) \\ \xi=\pm \end{array} }
\left[
\imath^{n^{(\xi)}_{i,j}} \cdot J_{n^{(\xi)}_{i,j}}\left(\frac{\imath}{2} {\mathcal X}^{\xi}_{i,j} \right)
\right] \\
\left. \right\} \quad (iia)
\end{eqnarray}
where the expression in curly brackets in $(iia)$ is summed over $(n_2,n_3;n_{2,3}^{+},n_{2,3}^{-}) \in {\mathbb Z}^4 $ subject to a constraint $2n_3 + 2(n_{2,3}^+-n_{2,3}^-)=0$ and to ${\mathcal N}:= 2 n_2+2(n_{2,3}^++n_{2,3}^-) $.
- Take $l_2=l_3 \neq l_1$. Then $\vec{n} = \left(n_1,n_2,0;n_{1,2}^+,n_{1,2}^-,0,0,0,0;(0)_{\xi=0}^3;(0)_{\xi=0}^3 \right)$. Then the result reads:
\begin{eqnarray}
&&I = \Delta(\vec{l}) \cdot e^{-\frac{1}{2} \sum\limits_{j=1}^3 {\mathcal A}_j l_j} \cdot \underline{(2\pi)^2 \cdot \frac{4 (-1)^{|{\mathcal N}|/2+1}}{{\mathcal N}^2-1} }\cdot \left\{ \right.\\
&&
\prod\limits_{j=1}^2 \left[\imath ^{n_j} \cdot J_{n_j}\left(\frac{\imath}{2} {\mathcal X}_j\right)\right] \cdot
\prod\limits_{\begin{array}{c} (i,j)=(1,2) \\ \xi=\pm \end{array} }
\left[
\imath^{n^{(\xi)}_{i,j}} \cdot J_{n^{(\xi)}_{i,j}}\left(\frac{\imath}{2} {\mathcal X}^{\xi}_{i,j} \right)
\right] \\
\left. \right\} \quad (iib)
\end{eqnarray}
where the expression in curly brackets in $(iib)$ is summed over $(n_1,n_2;n_{1,2}^{+},n_{1,2}^{-}) \in {\mathbb Z}^4 $ subject to a constraint $2n_1 + 2(n_{1,2}^++n_{1,2}^-)=0$ and to ${\mathcal N}:= 2 n_2+2(n_{1,2}^+-n_{1,2}^-) $.