(NOTE: Too long for comment)
(NOTE: I have utilized "Possible Closed forms" from WA in $J_1,J_3$)
$$ I = \int_{0}^{\frac{\pi}{2}} \left[\ln\left(\frac{e^{-x^2}}{\cos(x)} \left(1 + \cos(4x)\right)\right)\right]^2 \, dx $$
$$I=I_1+2I_2+I_3$$
We have $I_1, I_2$ ready one from OP's work and one from @Claude's work,
$$\boxed{I_1=\frac{\pi^5}{160}}$$
$$\boxed{I_2=\frac{-11}{32}\pi\zeta(3)}$$
We have,
$$I_3 = \int_{0}^{\frac{\pi}{2}} \left[\ln\left(\frac{1 + \cos(4x)}{\cos(x)}\right)\right]^2 \, dx = \int_{0}^{\frac{\pi}{2}} \left[\ln\left({1 + \cos(4x)}\right)-\ln(\cos x)\right]^2 \, dx $$
$$\int_{0}^{\frac{\pi}{2}} \ln^2\left({1 + \cos(4x)}\right)\,dx + \int_{0}^{\frac{\pi}{2}} \ln^2\left({ \cos(x)}\right)\,dx- 2 \int_{0}^{\frac{\pi}{2}}\ln(1+\cos(4x))\ln(\cos(x))\,dx $$
Using $1+\cos(4x)=2\cos^2(2x)$
$$\int_{0}^{\frac{\pi}{2}} \ln^2\left(2\cos^2(2x)\right)\,dx + \int_{0}^{\frac{\pi}{2}} \ln^2\left({ \cos(x)}\right)\,dx- 2\int_{0}^{\frac{\pi}{2}}\ln(2\cos^2(2x))\ln(\cos(x))\,dx $$
$$I_3=J_1+J_2-2J_3$$
$$\boxed{J_2=\frac{\pi^3}{24}+\frac{\pi}{2}\ln^2(2)}$$
$$J_1=\int_{0}^{\frac{\pi}{2}} \ln^2\left(2\cos^2(2x)\right)\,dx = \int_{0}^{\frac{\pi}{2}}\ln^2(2)+4\ln^2(\cos(2x))+4\ln(2) \ln(\cos(2x))\,dx$$
$$J_1=\frac{\pi}{2}\ln^2(2)+4\int_0^{\frac{\pi}{2}}\ln^2(\cos(2x))\,dx+4\ln(2)\int_0^{\frac{\pi}{2}}\ln(\cos(2x))\,dx$$
$$J_1=\frac{\pi}{2}\ln^2(2)+2\int_0^{\pi}\ln^2(\cos(x))\,dx++2\ln(2)\int_0^{\pi}\ln(\cos(x))\,dx$$
$$J_1=\frac{\pi}{2}\ln^2(2)+2J_2+2\int_{\frac{\pi}{2}}^{\pi}\ln^2(\cos(x))\,dx+2\ln(2)\int_0^{\frac{\pi}{2}}\ln(\cos(x))\,dx+2\ln(2)\int_{\frac{\pi}{2}}^{\pi}\ln(\cos(x))\,dx$$
$$\boxed{J_1 \approx \frac{\pi}{2}\ln^2(2)+2\left(\frac{\pi^3}{24}+\frac{\pi}{2}\ln^2(2)\right)+2\left(\frac14(-2\zeta(3)-2\zeta(5)-5\pi^2)+i(6h_4+13)\right)+2\ln(2)\left(-\frac{\pi}{2}\ln(2)\right)+2\ln(2)\left(\frac{i\pi}{2}(\pi+i\ln(2))\right)}$$
Where, $h_4$ is the fourth Hundred Dollar Challenge Constant
$$J_3 =\int_{0}^{\frac{\pi}{2}}\ln(2\cos^2(2x))\ln(\cos(x))\,dx$$
$$J_3 =\ln(2)\int_{0}^{\frac{\pi}{2}}\ln(\cos(x))\,dx+2\int_{0}^{\frac{\pi}{2}}\ln(\cos(x))\ln(\cos(2x))\,dx$$
$$J_3 =\ln(2)\left(-\frac{\pi}{2}\ln(2)\right)+2\int_{0}^{\frac{\pi}{2}}\ln(\cos(x))\ln(\cos(2x))\,dx$$
$$\boxed{J_3 \approx \ln(2)\left(-\frac{\pi}{2}\ln(2)\right)+\left(\frac{49}{2\pi^4}\right)+2\left(-\frac{e^{1+3e-2\pi}}{\pi^{1+e}}\tan(e\pi)+i\left(43C_{KL}-80\right)\right)}$$
Where, $C_{KL}$ is Komornik-Loreti Constant
So to summarize,
$$I \approx \frac{\pi^5}{160}-\frac{11}{16}\pi\zeta(3)+( big\,\, mess)$$
$$I_{21} = -2 \int_0^{\pi/4} x^2 \ln(1 + \cos(4x)) , dx - 2 \int_{\pi/4}^{\pi/2} x^2 \ln(1 + \cos(4x)) , dx.$$ $$ I_{211} = -\frac{1}{4} \int_0^{\pi/2} u^2 \ln(1 + \cos(2u)) , du = -\frac{1}{4} \int_0^{\pi/2} u^2 \ln(2\cos^2 u) , du $$
$$ = -\frac{1}{4} \int_0^{\pi/2} u^2 \left[\ln(2) + \ln(\cos^2 u)\right] , du $$
$$ = -\frac{\ln(2)}{4} \int_0^{\pi/2} u^2 , du - \frac{1}{4} \int_0^{\pi/2} u^2 \ln(\cos^2 u) , du $$
– Martin.s Aug 31 '24 at 08:37