That’s because Much like the New Wolfenstein games, Doom is running on current OpenGL and Vulkan – neither of witch vorpX supports yet.
Only older OpenGL titles (up until the last Amnesia as I’ve heard) can work properly in 3D.
I tried Doom a couple years ago, and it was as you described, real eye-strain. Seems like there were more posts about this from earlier this year. Some claimed it’s better now, but I haven’t checked for myself. I have my doubts though unless we hear further from Ralf.
If nothing else, you could disable 3D and see if playing 2D is any fun.