I get eyestrain with every Linux I use when the X-Server is active.
Maybe the font rendering uses temporal dithering.
Not sure how to get more information about that.
Even with Nvidia proprietary drivers and dithering disabled (in said driver), I get Linux eye strain.
My only explanation so far is either forced temporal dithering from other sources than the driver that are still unknown (X.Org, font rendering, ...?) or issues we didn't think about yet like vertical sync or other video mode aspects.
I tried countless distributions, and they all have the X-Server in common. 2 weeks ago I tried Arch Linux, it starts pretty much from the scratch, showing just a command line. But that command line is no ordinary command line video mode. It's full HD 1920x1080 and, for me, triggers eye strain. Allthough it's just a few pixels of seemingly static command line text. My Linux knowledge is not too deep so I couldn't track this further down. BTW: same on the Raspberry Pi command line (Full HD), which uses a totally different graphics unit. So it might be a software problem.
Perhaps the upcoming Wayland might solve the issues.