$(A)\enspace$ Dissolving the integral
With the split
$\displaystyle \frac{\tanh x}{x^2}-\frac{1}{x e^{2x}} =$
$\displaystyle =\left( \frac{2}{e^{2x}} -\frac{1}{e^{4x}} -\frac{1}{e^x} \right) \frac{1}{x} - \frac{e^{2x}-1}{e^{4x} (e^{2x}+1)} \frac{1}{x} + \frac{1}{e^{2x}+1} \frac{e^{2x}-1-2x}{x^2} + \frac{1}{x e^x} - \frac{1}{x e^{2x}} $
follows:
$\displaystyle \int\limits_0^\infty \left(\frac{\tanh x}{x^2}-\frac{1}{x e^{2x}}\right) dx = \int\limits_0^\infty \left( \frac{2}{e^{2x}} -\frac{1}{e^{4x}} -\frac{1}{e^x} \right) \frac{dx}{x} - \int\limits_0^\infty \frac{e^{2x}-1}{e^{4x} (e^{2x}+1)} \frac{dx}{x} + $
$\hspace{5cm}\displaystyle +\int\limits_0^\infty \frac{1}{e^{2x}+1} \sum\limits_{n=2}^\infty \frac{2^n x^{n-2}}{n!} dx + \int\limits_0^\infty \left(\frac{1}{x e^x} - \frac{1}{x e^{2x}}\right) dx =$
$\displaystyle = \text{Ei}(0)\cdot (2-1-1) - \int\limits_0^\infty \frac{(1-e^{-ax})(1-e^{-bx})}{x(e^x-1)}dx |_{a=b=\frac{1}{2}} + \sum\limits_{n=2}^\infty \frac{2^n}{n!} \int\limits_0^\infty \frac{x^{n-2}}{e^{2x}+1} dx + \ln 2 $
$\displaystyle = 0 + \ln\frac{\Gamma(1+a)\Gamma(1+b)}{\Gamma(1+a+b)} |_{a=b=\frac{1}{2}} +
\sum\limits_{k=2}^\infty \frac{2^k}{k!}\eta(k-1)\Gamma(k-1)2^{1-k} + \ln 2 $
$\displaystyle = 2\ln2 + \ln\frac{\pi}{4} + 2 \sum\limits_{n=2}^\infty \frac{\eta(n)}{n(n+1)} $
$(B)\enspace$ Basics
The following calculation of $\enspace\displaystyle \sum\limits_{n=2}^\infty \frac{\eta(n)}{n(n+1)}\enspace $ is based on a generalization of the Gamma function,
called $Q_m(x)$ in https://www.fernuni-hagen.de/analysis/download/bachelorarbeit_aschauer.pdf
,
with $\enspace\displaystyle \ln Q_m(x)=\frac{(-x)^{m+1}}{m+1}\gamma +\sum\limits_{n=2}^\infty\frac{(-x)^{m+n}}{m+n}\zeta(n)\enspace$ on page $13$, $(4.2)\,$ .
A modification is $\enspace\displaystyle Q_m^*(x):=(1+x)Q_m(x)\enspace$ on page $24$, $(4.8)$ and $(4.9)$ .
Special values which are used here are $\,Q_0^*(-1)=1\,$, $\,\displaystyle Q_1^*(-1)=\frac{1}{\sqrt{2\pi}}\,$ ,
$\displaystyle Q_0(-\frac{1}{2})=\Gamma(\frac{1}{2})=\sqrt{\pi}\,$
and $\,\displaystyle Q_1(-\frac{1}{2})=A^{\frac{3}{2}}2^{-\frac{7}{24}}\,$ (page $38$) .
With the generalized Glaisher-Kinkelin constant $\,A_n\,$ it’s $\,A:=A_1\,$ .
Note: $\enspace\displaystyle Q_0(x)=\Gamma(1+x)\,$ , $\enspace\displaystyle Q_1(x)=\frac{\sqrt{2\pi}^x}{e^{\frac{1}{2}x(x+1)}G(1+x)}\,$ ($G$ is the Barnes G function)
$\hspace{1.4cm}$Special value: $\enspace\displaystyle G(\frac{1}{2})=2^\frac{1}{24}e^\frac{1}{8}\pi^{-\frac{1}{4}}A^{-\frac{3}{2}}$
$(C)\enspace$ Calculating the series
$\displaystyle \sum\limits_{n=2}^\infty \frac{x^n}{n(n+1)} \eta(n) =$
$\displaystyle =\left(\sum\limits_{n=2}^\infty \frac{x^n}{n} \zeta(n) - \sum\limits_{n=2}^\infty \frac{x^n}{n+1} \zeta(n)\right) - 2 \left(\sum\limits_{n=2}^\infty \frac{x^n}{2^n n} \zeta(n) - \sum\limits_{n=2}^\infty \frac{x^n}{2^n (n+1)} \zeta(n)\right) $
$\displaystyle = \left(\ln Q_0(-x) - x\gamma - \frac{1}{x}(\ln Q_1(-x)-\frac{x^2}{2}\gamma) \right) $
$\hspace{0.5cm}\displaystyle - 2 \left(\ln Q_0(-\frac{x}{2} ) - \frac{x}{2}\gamma - \frac{2}{x}(\ln Q_1(-\frac{x}{2})-\frac{x^2}{8}\gamma) \right) $
$\displaystyle = \ln Q_0^*(-x) - \frac{1}{x}\ln Q_1^*(-x) + \frac{1-x}{x}\ln(1-x) - 2 \ln Q_0(-\frac{x}{2}) + \frac{4}{x}\ln Q_1(-\frac{x}{2}) $
With $\,x\uparrow 1\,$ follows
$ \displaystyle \sum\limits_{n=2}^\infty \frac{\eta(n)}{n(n+1)} = \ln Q_0^*(-1) - \ln Q_1^*(-1) - 2 \ln Q_0(-\frac{1}{2}) + 4 Q_1(-\frac{1}{2}) $
$\hspace{2.5cm}\displaystyle = -\frac{2}{3}\ln 2 - \frac{1}{2}\ln \pi + 6 \ln A $
and therefore
$\displaystyle \int\limits_0^\infty \left(\frac{\tanh x}{x^2}-\frac{1}{x e^{2x}}\right) dx = 2\ln2 + \ln\frac{\pi}{4} + 2 \left(-\frac{2}{3}\ln 2 - \frac{1}{2}\ln \pi + 6 \ln A \right) $
$\hspace{4.5cm}\displaystyle = 12 \ln A - \frac{4}{3}\ln 2 \enspace$ .