Let $I$ denote the integral
$$I:=\int_{1}^{\phi}\frac{x^{2}+1}{x^{4}-x^{2}+1}\ln{\left(1+x-\frac{1}{x}\right)}\,\mathrm{d}x,$$
with $\phi$ of course being the golden ratio, $\phi=\frac{1+\sqrt{5}}{2}$.
As a numerical approximation, we find
$$I\approx0.272198.$$
Try substituting instead
$$\frac12\left(x-\frac{1}{x}\right)=t,$$
$$\implies\frac12\left(1+\frac{1}{x^{2}}\right)\,\mathrm{d}x=\mathrm{d}t.$$
Taking the square, we have
$$\frac14\left(x^{2}-2+\frac{1}{x^{2}}\right)=t^{2}.$$
Then,
$$\begin{align}
I
&=\int_{1}^{\phi}\frac{x^{2}+1}{x^{4}-x^{2}+1}\ln{\left(1+x-\frac{1}{x}\right)}\,\mathrm{d}x\\
&=\int_{1}^{\phi}\frac{2x^{2}}{x^{4}-x^{2}+1}\ln{\left(1+x-\frac{1}{x}\right)}\,\frac{x^{2}+1}{2x^{2}}\,\mathrm{d}x\\
&=\int_{1}^{\phi}\frac{2}{\left(x^{2}-2+x^{-2}\right)+1}\ln{\left(1+x-\frac{1}{x}\right)}\,\frac12\left(1+\frac{1}{x^{2}}\right)\,\mathrm{d}x\\
&=\int_{0}^{\frac12}\frac{2}{4t^{2}+1}\ln{\left(1+2t\right)}\,\mathrm{d}t;~~~\small{\left[\frac12\left(x-\frac{1}{x}\right)=t\right]}\\
&=\int_{0}^{1}\frac{\ln{\left(1+u\right)}}{u^{2}+1}\,\mathrm{d}u;~~~\small{\left[2t=u\right]}.\\
\end{align}$$
Expressing the logarithmic term as an integral, $I$ becomes a double integral. Changing the order of integration, we obtain
$$\begin{align}
I
&=\int_{0}^{1}\frac{\ln{\left(1+x\right)}}{1+x^{2}}\,\mathrm{d}x\\
&=\int_{0}^{1}\frac{\mathrm{d}x}{1+x^{2}}\int_{0}^{1}\mathrm{d}t\,\frac{x}{1+xt}\\
&=\int_{0}^{1}\mathrm{d}x\int_{0}^{1}\mathrm{d}t\,\frac{x}{\left(1+x^{2}\right)\left(1+xt\right)}\\
&=\int_{0}^{1}\mathrm{d}t\int_{0}^{1}\mathrm{d}x\,\frac{x}{\left(1+x^{2}\right)\left(1+tx\right)}\\
&=\int_{0}^{1}\mathrm{d}t\int_{0}^{1}\mathrm{d}x\,\left[\frac{t+x}{\left(1+t^{2}\right)\left(1+x^{2}\right)}-\frac{t}{\left(1+t^{2}\right)\left(1+tx\right)}\right];~~~\small{P.F.D.}\\
&=\int_{0}^{1}\frac{\mathrm{d}t}{\left(1+t^{2}\right)}\int_{0}^{1}\mathrm{d}x\,\left[\frac{t+x}{\left(1+x^{2}\right)}-\frac{t}{\left(1+tx\right)}\right]\\
&=\int_{0}^{1}\frac{\mathrm{d}t}{\left(1+t^{2}\right)}\left[\int_{0}^{1}\mathrm{d}x\,\frac{t}{\left(1+x^{2}\right)}+\int_{0}^{1}\mathrm{d}x\,\frac{x}{\left(1+x^{2}\right)}-\int_{0}^{1}\mathrm{d}x\,\frac{t}{\left(1+tx\right)}\right]\\
&=\int_{0}^{1}\frac{\mathrm{d}t}{\left(1+t^{2}\right)}\left[\frac{\pi}{4}t+\frac12\ln{\left(2\right)}-\ln{\left(1+t\right)}\right]\\
&=\int_{0}^{1}\frac{\mathrm{d}t}{\left(1+t^{2}\right)}\left[\frac{\pi}{4}t+\frac12\ln{\left(2\right)}\right]-\int_{0}^{1}\frac{\ln{\left(1+t\right)}}{1+t^{2}}\,\mathrm{d}t\\
&=\frac{\pi}{4}\ln{\left(2\right)}-I.\\
\end{align}$$
Thus,
$$I=\frac{\pi}{8}\ln{\left(2\right)}.\blacksquare$$