Update: I have managed to explain the simplifications.
We claim
$$
\int_0^1\log(k+1-k^x)+2\log(1+k^x)\,dx=2\log(k+1)
$$Indeed, if this is the case, we are left with the sum
$$
\sum_{k=0}^{\infty}\frac{(-1)^{k+1} \log(k+1)}{(k+1)^2}=\eta'(2)=\eta(2)\left(\gamma+\log\left(\frac{4\pi}{A^{12}}\right)\right);
$$this can be shown, for instance, on this MSE post. Now we have to prove the claim. We have
$$
\int _0^1 \log(k+1-k^x)\,dx =\log(k+1)+ \frac{\text{Li}_2\left(\frac{1}{k+1}\right)-\text{Li}_2\left(\frac{k}{k+1}\right) }{\log (k)};
$$
$$
2\int _0^1 \log(1+k^x)\,dx =-\frac{2 \text{Li}_2(-k)+\frac{\pi ^2}{6}}{ \log (k)};
$$Combining, we have
$$\int _0^1 \log(k+1-k^x)+2\log(1+x^k)\,dx $$
$$
=\log(k+1)+\underbrace{\frac{\text{Li}_2\left(\frac{1}{k+1}\right)-\text{Li}_2\left(\frac{k}{k+1}\right)-2 \text{Li}_2(-k)-\frac{\pi ^2}{6}}{\log (k)}}_{\color{red}{L(k)}}
$$Let's show $L(k)=\log(k+1)$. We will use two functional identities which can be found here. First, we'll use Euler's reflection formula to eliminate $\text{Li}_2\left(\frac{k}{k+1}\right)$:
$$
\text{Li}_2(z)=-\text{Li}_2(1-z)-\log (1-z) \log (z)+\frac{\pi ^2}{6};
$$
$$
L(k) = \frac{-2 \text{Li}_2(-k)+2 \text{Li}_2\left(\frac{1}{k+1}\right)+\log \left(\frac{1}{k+1}\right) \log
\left(\frac{k}{k+1}\right)-\frac{\pi ^2}{3}}{\log(k)}
$$
Next, use an inversion formula, valid for $\Re(z)\le 0$ with $z=-k$:
$$\text{Li}_2(z)=\text{Li}_2\left(\frac{1}{1-z}\right)+\frac{1}{2} \log (1-z) \log
\left(\frac{1-z}{z^2}\right)-\frac{\pi ^2}{6};
$$
$$
L(k) = \frac{\log \left(\frac{1}{k+1}\right) \log \left(\frac{k}{k+1}\right)-\log (k+1) \log
\left(\frac{k+1}{k^2}\right)}{\log(k)}
$$
$$
= \frac{ \log (k+1)\log \left(\frac{k+1}{k}\right)+\log (k+1) \log \left(\frac{k^2}{k+1}\right)}{\log(k)}
$$
$$
= \frac{ \log (k+1)\log \left(\frac{k+1}{k}\cdot \frac{k^2}{k+1}\right)}{\log(k)}
$$
$$
=\log(k+1),
$$as was to be shown.