Here is my route in large steps
Consider the integral found in the OP
$$\eta \left(2\right)-\overline{H}_k^{\left(2\right)}=-4\int _0^1\left(-x^2\right)^k\frac{x\ln \left(x\right)}{1+x^2}\:dx,$$
as well as the generating function
$$\sum _{k=1}^{\infty }\frac{H_k}{2k+1}x^{2k}=\frac{1}{2x}\left(\ln \left(2\right)+\frac{1}{2}\ln \left(1-x^2\right)\right)\ln \left(\frac{1-x}{1+x}\right)+\frac{1}{2x}\left(\operatorname{Li}_2\left(\frac{1+x}{2}\right)-\operatorname{Li}_2\left(\frac{1-x}{2}\right)\right).$$
Replacing $x\rightarrow ix$, multiplying both sides by $-4\frac{x\ln \left(x\right)}{1+x^2}$ and integrating from $0$ to $1$ with respect to $x$ yields
$$\sum _{k=1}^{\infty }\frac{H_k}{2k+1}\left(\eta \left(2\right)-\overline{H}_k^{\left(2\right)}\right)=4\int _0^1\frac{\left(\ln \left(2\right)+\frac{1}{2}\ln \left(1+x^2\right)\right)\arctan \left(x\right)\ln \left(x\right)}{1+x^2}\:dx$$
$$+2i\int _0^1\left(\operatorname{Li}_2\left(\frac{1+ix}{2}\right)-\operatorname{Li}_2\left(\frac{1-ix}{2}\right)\right)\frac{\ln \left(x\right)}{1+x^2}\:dx$$
$$=4\int _0^1\frac{\left(\ln \left(2\right)+\frac{1}{2}\ln \left(1+x^2\right)\right)\arctan \left(x\right)\ln \left(x\right)}{1+x^2}\:dx+4\Re \left\{i\int _0^1\frac{\ln \left(x\right)\operatorname{Li}_2\left(\frac{1+ix}{2}\right)}{1+x^2}\:dx\right\}.$$
Integrating by parts the $2$nd integral and taking the real part leads to
$$\Re \left\{i\int _0^1\frac{\ln \left(x\right)\operatorname{Li}_2\left(\frac{1+ix}{2}\right)}{1+x^2}\:dx\right\}$$
$$=G^2-\frac{\pi }{8}\ln \left(2\right)G-\int _0^1\frac{\arctan \left(x\right)\ln \left(x\right)\left(\frac{1}{2}\ln \left(1+x^2\right)-x\arctan \left(x\right)-\ln \left(2\right)\right)}{1+x^2}\:dx$$
$$+\int _0^1\frac{\left(\frac{1}{2}\ln \left(1+x^2\right)-x\arctan \left(x\right)-\ln \left(2\right)\right)\operatorname{Ti}_2\left(x\right)}{1+x^2}\:dx,$$
and this means that
$$\sum _{k=1}^{\infty }\frac{H_k}{2k+1}\left(\eta \left(2\right)-\overline{H}_k^{\left(2\right)}\right)$$
$$=4G^2-\frac{\pi }{2}\ln \left(2\right)G+8\ln \left(2\right)\int _0^1\frac{\arctan \left(x\right)\ln \left(x\right)}{1+x^2}\:dx+4\int _0^1\frac{x\arctan ^2\left(x\right)\ln \left(x\right)}{1+x^2}\:dx$$
$$+4\int _0^1\frac{\left(\frac{1}{2}\ln \left(1+x^2\right)-x\arctan \left(x\right)-\ln \left(2\right)\right)\operatorname{Ti}_2\left(x\right)}{1+x^2}\:dx$$
$$=4G^2-\pi \ln \left(2\right)G+8\ln \left(2\right)\int _0^{\frac{\pi }{4}}x\ln \left(\tan \left(x\right)\right)\:dx+8\int _0^{\frac{\pi }{4}}x\ln \left(\sin \left(x\right)\right)\ln \left(\cos \left(x\right)\right)\:dx$$
$$-8\int _0^{\frac{\pi }{4}}x\ln ^2\left(\cos \left(x\right)\right)\:dx-8\underbrace{\int _0^{\frac{\pi }{4}}\operatorname{Ti}_2\left(\tan \left(x\right)\right)\ln \left(\cos \left(x\right)\right)\:dx}_{I_1}-4\ln \left(2\right)\underbrace{\int _0^1\frac{\operatorname{Ti}_2\left(x\right)}{1+x^2}\:dx}_{I_2}.$$
Next, it's time for $2$ observations.
In order to reduce $I_1$ we must first consider
$$\int _0^{\frac{\pi }{4}}\sin \left(2\left(2k+1\right)x\right)\ln \left(\cos \left(x\right)\right)\:dx=-\frac{1}{4}\left(\frac{-\overline{H}_k+2H_{2k}-2H_k-\ln \left(2\right)}{2k+1}+\frac{1}{\left(2k+1\right)^2}\right),$$
with this it becomes
$$\int _0^{\frac{\pi }{4}}\operatorname{Ti}_2\left(\tan \left(x\right)\right)\ln \left(\cos \left(x\right)\right)\:dx=\sum _{k=0}^{\infty }\frac{1}{\left(2k+1\right)^2}\int _0^{\frac{\pi }{4}}\sin \left(2\left(2k+1\right)x\right)\ln \left(\cos \left(x\right)\right)\:dx$$
$$+\int _0^{\frac{\pi }{4}}x\ln \left(\sin \left(x\right)\right)\ln \left(\cos \left(x\right)\right)\:dx-\int _0^{\frac{\pi }{4}}x\ln ^2\left(\cos \left(x\right)\right)\:dx$$
$$=\frac{1}{4}\sum _{k=1}^{\infty }\frac{\overline{H}_k-2H_{2k}+2H_k}{\left(2k+1\right)^3}-\frac{15}{64}\zeta \left(4\right)+\frac{7}{32}\ln \left(2\right)\zeta \left(3\right)+\int _0^{\frac{\pi }{4}}x\ln \left(\sin \left(x\right)\right)\ln \left(\cos \left(x\right)\right)\:dx$$
$$-\int _0^{\frac{\pi }{4}}x\ln ^2\left(\cos \left(x\right)\right)\:dx.$$
Secondly, $I_2$ becomes
$$\int _0^1\frac{\operatorname{Ti}_2\left(x\right)}{1+x^2}\:dx=\frac{\pi }{4}G+2\int _0^{\frac{\pi }{4}}x\ln \left(\tan \left(x\right)\right)\:dx.$$
Replacing everything from before we obtain
$$\sum _{k=1}^{\infty }\frac{H_k}{2k+1}\left(\eta \left(2\right)-\overline{H}_k^{\left(2\right)}\right)=4G^2-2\pi \ln \left(2\right)G+\frac{5}{8}\zeta \left(4\right)-\frac{7}{4}\ln \left(2\right)\zeta \left(3\right)-2\sum _{k=1}^{\infty }\frac{\overline{H}_k}{\left(2k+1\right)^3}$$
$$-2\sum _{k=1}^{\infty }\frac{\left(-1\right)^kH_k}{k^3}-4\sum _{k=1}^{\infty }\frac{H_k}{\left(2k+1\right)^3},$$
and given that the resulting series are either known or easily relatable to simple integrals, we conclude with
$$\sum _{k=1}^{\infty }\frac{H_k}{2k+1}\left(\eta \left(2\right)-\overline{H}_k^{\left(2\right)}\right)$$
$$=2G^2-2\pi \ln \left(2\right)G+\frac{53}{16}\zeta \left(4\right)-4\operatorname{Li}_4\left(\frac{1}{2}\right)+\ln ^2\left(2\right)\zeta \left(2\right)-\frac{1}{6}\ln ^4\left(2\right).$$
Unfortunately, the imaginary unit was briefly involved and therefore everything started with pretty complicated terms. Interestingly enough, all the rough integrals cancelled and the last relation only featured very simple or known series.
Perhaps there's a way to use some of the ideas presented here to further simplify the already given approach.