Different Solution with a big bonus:
First lets define the following:
$$M=\sum_{n=1}^\infty\frac{H_n^2}{n^32^n}$$
$$N=\sum_{n=1}^\infty\frac{H_n^{(2)}}{n^32^n}$$
I am going to establish two relations of $M$ and $N$ and solve them as a system of equations.
The first relation:
In the question body, we reached
$$M+N=\int_0^1\frac{\ln^2(1-x)\operatorname{Li}_2(x/2)}{x}dx$$
and by using $\quad\displaystyle\frac{\operatorname{Li}_2(x)}{x}=-\int_0^1\frac{\ln y}{1-xy}dy\quad$ we can write
$$M+N=-\frac12\int_0^1\ln y\left[\int_0^1\frac{\ln^2(1-x)}{1-(y/2)x}dx\right]dy$$
$$=2\int_0^1\frac{\ln y}{y}\operatorname{Li}_3\left(\frac{y}{y-2}\right)dy\overset{IBP}{=}-\int_0^1\frac{\operatorname{Li}_2(-y)}{y}\ln^2\left(\frac{2y}{1+y}\right)dy$$
$$\small{=-\int_0^1\frac{\operatorname{Li}_2(-y)}{y}\left[\ln^22+2\ln2\ln y+\ln^2y-2\ln2\ln(1+y)-2\ln y\ln(1+y)+\ln^2(1+y)\right]dy}$$
$$=-\ln^22\underbrace{\int_0^1\frac{\operatorname{Li}_2(-y)}{y}dy}_{I_1}-2\ln2\underbrace{\int_0^1\frac{\operatorname{Li}_2(-y)\ln y}{y}dy}_{I_2}-\underbrace{\int_0^1\frac{\operatorname{Li}_2(-y)\ln^2y}{y}dy}_{I_3}\\+2\ln2\underbrace{\int_0^1\frac{\operatorname{Li}_2(-y)\ln(1+y)}{y}dy}_{I_4}+2\underbrace{\int_0^1\frac{\operatorname{Li}_2(-y)\ln y\ln(1+y)}{y}dy}_{I_5}-\underbrace{\int_0^1\frac{\operatorname{Li}_2(-y)\ln^2(1+y)}{y}dy}_{I_6}$$
$$I_1=\operatorname{Li}_3(-1)=-\frac34\zeta(3)$$
$$I_2\overset{IBP}{=}-\int_0^1\frac{\operatorname{Li}_3(-y)}{y}dy=-\operatorname{Li}_4(-1)=\frac78\zeta(4)$$
$$I_3\overset{IBP}{=}-2\int_0^1\frac{\operatorname{Li}_3(-y)\ln y}{y}dy\overset{IBP}{=}2\int_0^1\frac{\operatorname{Li}_4(-y)}{y}dy=2\operatorname{Li}_5(-1)=-\frac{15}8\zeta(5)$$
$$I_4=-\frac12\operatorname{Li}_2^2(-1)=-\frac5{16}\zeta(4)$$
$$I_5\overset{IBP}{=}\frac12\int_0^1\frac{\operatorname{Li}_2^2(-y)}{y}dy=\frac38\zeta(2)\zeta(3)-\frac{17}{32}\zeta(5)$$
where the last result follows from this solution, check Eq$(3)$
$I_6$ is elegantly evaluated by Cornel here in page $5$ and by me here,
$$\small{I_6=4\operatorname{Li}_5\left(\frac12\right)+4\ln2\operatorname{Li}_4\left(\frac12\right)-\frac{125}{32}\zeta(5)-\frac{1}{8}\zeta(2)\zeta(3)+\frac{7}{4}\ln^22\zeta(3)-\frac2{3}\ln^32\zeta(2)+\frac{2}{15}\ln^52}$$
Combine these results to obtain
$$M+N=-4\operatorname{Li}_5\left(\frac12\right)-4\ln2\operatorname{Li}_4\left(\frac12\right)+\frac{131}{32}\zeta(5)$$
$$-\frac{19}{8}\ln2\zeta(4)+\frac{7}{8}\zeta(2)\zeta(3)-\ln^22\zeta(3)+\frac2{3}\ln^32\zeta(2)-\frac{2}{15}\ln^52\tag1$$
The second relation:
From here
$$\frac{\ln^2(1-x)}{1-x}=\sum_{n=1}^\infty x^n\left(H_n^2-H_n^{(2)}\right)\tag2$$
multiply both sides by $\frac{\ln^2x}{x}$ then integrate from $x=0$ to $1/2$
we have
\begin{align}
I&=\int_0^{1/2}\frac{\ln^2(1-x)\ln^2x}{x(1-x)}\ dx=\sum_{n=1}^\infty\left(H_n^2-H_n^{(2)}\right)\int_0^{1/2}x^{n-1}\ln^2x\ dx\\
&=\sum_{n=1}^\infty\left(H_n^2-H_n^{(2)}\right)\left(\frac{\ln^22}{n2^n}+\frac{2\ln2}{n^22^n}+\frac{2}{n^32^n}\right)\\
&=\ln^22\sum_{n=1}^\infty\frac{H_n^2-H_n^{(2)}}{n2^n}+2\ln2\sum_{n=1}^\infty\frac{H_n^2-H_n^{(2)}}{n^22^n}+2\sum_{n=1}^\infty\frac{H_n^2}{n^32^n}-2\sum_{n=1}^\infty\frac{H_n^{(2)}}{n^32^n}\\
&=\ln^22S_1+2\ln2S_2+2M-2N
\end{align}
Or
$$M-N=\frac12I-\frac12\ln^22S_1-\ln2S_2$$
Evaluation of $I:$
\begin{align}
I&=\int_0^{1/2}\frac{\ln^2(1-x)\ln^2x}{x(1-x)}\ dx\overset{1-x\mapsto x}{=}\int_{1/2}^1\frac{\ln^2(1-x)\ln^2x}{x(1-x)}\ dx\\
2I&=\int_0^{1}\frac{\ln^2(1-x)\ln^2x}{x(1-x)}\ dx=\int_0^{1}\frac{\ln^2(1-x)\ln^2x}{x}\ dx+\underbrace{\int_0^{1}\frac{\ln^2(1-x)\ln^2x}{1-x}\ dx}_{1-x\mapsto x}\\
I&=\int_0^{1}\frac{\ln^2(1-x)\ln^2x}{x}\ dx=2\sum_{n=1}^\infty\frac{H_n}{n+1}\int_0^1x^n\ln^2x\ dx\\
&=4\sum_{n=1}^\infty\frac{H_n}{(n+1)^4}=4\sum_{n=1}^\infty\frac{H_n}{n^4}-4\zeta(5)=8\zeta(5)-4\zeta(2)\zeta(3)
\end{align}
Evaluation of $S_1$:
Divide both sides of (2) by $x$ then integrate from $x=0$ to $1/2$ and use the fact that $\int_0^{1/2}x^{n-1}=\frac1{n2^n}$
\begin{align}
S_1&=\sum_{n=1}^\infty \frac{H_n^2-H_n^{(2)}}{n2^n}=\int_0^{1/2}\frac{\ln^2(1-x)}{x(1-x)}\ dx\\
&=\int_{1/2}^{1}\frac{\ln^2x}{x(1-x)}\ dx=\sum_{n=0}^\infty\int_{1/2}^1x^{n-1}\ln^2x\ dx\\
&=\frac13\ln^32+\sum_{n=1}^\infty\int_{1/2}^1x^{n-1}\ln^2x\ dx\\
&=\frac13\ln^32+\sum_{n=1}^\infty\left(\frac2{n^3}-\frac{\ln^22}{n2^n}-\frac{2\ln2}{n^22^n}-\frac{2}{n^32^n}\right)\\
&=\frac13\ln^32+2\zeta(3)-\ln^32-2\ln2\operatorname{Li}_2\left(\frac12\right)-2\operatorname{Li}_3\left(\frac12\right)=\frac14\zeta(3)
\end{align}
where we used $\operatorname{Li}_2\left(\frac12\right)=\frac12\zeta(2)-\frac12\ln^22$ and $\operatorname{Li}_3\left(\frac12\right)=\frac78\zeta(3)-\frac12\ln2\zeta(2)+\frac16\ln^32$
Evaluation of $S_2$:
integrate both sides of (2) from $x=0$ to $x$ to have
$$-\frac13\ln^3(1-x)=\sum_{n=1}^\infty\frac{x^{n+1}}{n+1}\left(H_n^2-H_n^{(2)}\right)=\sum_{n=1}^\infty\frac{x^{n}}{n}\left(H_n^2-H_n^{(2)}-\frac{2H_n}{n}+\frac{2}{n^2}\right)\tag{3}$$
Now divide both sides of (3) by $x$ then integrate from $x=0$ to $1/2$ and use the fact that $\int_0^{1/2}x^{n-1}=\frac1{n2^n}$
$$-\frac13\int_0^{1/2}\frac{\ln^3(1-x)}{x}\ dx=\sum_{n=1}^\infty\frac{1}{n^22^n}\left(H_n^2-H_n^{(2)}-\frac{2H_n}{n}+\frac{2}{n^2}\right)$$
Rearranging the terms
$$S_2=\sum_{n=1}^\infty\frac{H_n^2-H_n^{(2)}}{n^22^n}=2\sum_{n=1}^\infty\frac{H_n}{n^32^n}-\frac13\int_0^{1/2}\frac{\ln^3(1-x)}{x}\ dx-2\operatorname{Li}_4\left(\frac12\right)$$
Substitute
$$\sum_{n=1}^\infty \frac{H_n}{2^nn^3}=\operatorname{Li}_4\left(\frac12\right)+\frac18\zeta(4)-\frac18\ln2\zeta(3)+\frac1{24}\ln^42$$
and
\begin{align}
\int_0^{1/2}\frac{\ln^3(1-x)}{x}\ dx&=\int_{1/2}^{1}\frac{\ln^3x}{1-x}\ dx\\
&=\sum_{n=1}^\infty\int_{1/2}^1 x^{n-1}\ln^3x\ dx\\
&=\sum_{n=1}^\infty\left(\frac{\ln^32}{n2^n}+\frac{3\ln^22}{n^22^n}+\frac{6\ln2}{n^32^n}+\frac{6}{n^42^n}-\frac{6}{n^4}\right)\\
&=\ln^42+3\ln^32\operatorname{Li}_2\left(\frac12\right)+6\ln2\operatorname{Li}_3\left(\frac12\right)+6\operatorname{Li}_4\left(\frac12\right)-6\zeta(4)\\
&=6\operatorname{Li}_4\left(\frac12\right)-6\zeta(4)+\frac{21}4\ln2\zeta(3)-\frac32\ln^22\zeta(2)+\frac12\ln^42
\end{align}
we get
$$S_2=-2\operatorname{Li}_4\left(\frac12\right)+\frac94\zeta(4)-2\ln2\zeta(3)+\frac12\ln^22\zeta(2)-\frac1{12}\ln^42$$
collect the results of $I$, $S_1$ and $S_2$ we get
$$M-N=2\ln2\operatorname{Li}_4\left(\frac12\right)+4\zeta(5)$$
$$-\frac{9}{4}\ln2\zeta(4)-2\zeta(2)\zeta(3)+\frac{15}8\ln^22\zeta(3)-\frac1{2}\ln^32\zeta(2)+\frac{1}{12}\ln^52\tag4$$
Now we are ready to calculate the two sums:
$$M=\frac{(1)+(4)}{2}=-2\operatorname{Li}_5\left(\frac12\right)-\ln2\operatorname{Li}_4\left(\frac12\right)+\frac{279}{64}\zeta(5)-\frac{37}{16}\ln2\zeta(4)-\frac{9}{16}\zeta(2)\zeta(3)\\+\frac{7}{16}\ln^22\zeta(3)+\frac1{12}\ln^32\zeta(2)-\frac{1}{40}\ln^52$$
$$N=\frac{(1)-(4)}{2}=-2\operatorname{Li}_5\left(\frac12\right)-3\ln2\operatorname{Li}_4\left(\frac12\right)+\frac{23}{64}\zeta(5)-\frac1{16}\ln2\zeta(4)+\frac{23}{16}\zeta(2)\zeta(3)\\-\frac{23}{16}\ln^22\zeta(3)+\frac7{12}\ln^32\zeta(2)-\frac{13}{120}\ln^52$$