I had this small Linux eye strain with any GPU/device/display I have tried so far. Even with ARM boards like Raspberry Pi, ODROID... which have GPUs different from Intel, AMD, Nvidia. As you say the eye strain is not super strong like in modern Windows, but it's there, and for me accumulates over time. Looking at Internet browsers, as usual, is even worse.
It might still (partially?) be a matter of just finding the right GPU/device, but I can't dismiss the idea that Linux in general does something, when directly connected, that is unnecessary and causing eye strain. I currently (on Android TV) use a Linux distro (Armbian) over the network via a known-good VNC connection, that, as I don't have any eye strain, obviously does not transmit those eye-strain-inducing signals (whatever they are). The downside is that I can't do anything that requires fast video update (YouTube etc.), but at least I can use a desktop, office programs, and browse the Internet with any browser without having eye strain.
I should mention that deactivating temporal dithering via xrandr (nouveau), Nvidia-X-Settings, Raspberry Pi boot file, provided those settings truly disable all dithering, did not fix this Linux eye strain issue for me.
The open source nouveau driver for me was better than the official Nvidia one. Might be worth to always test both of them on a new hardware setup.