I still get small eye strain in Linux, using the X Server and in some cases at the command line, too.
I believe it is a driver issue, because I don't have any problems in Windows using the same hardware.
I could only test my NVIDIA card and my Raspberry Pi, but they both produce the same effect in various Linux distributions, including Arch.
Raspberry Pi on RiscOS: no eye strain at all, but it is not a usable OS.
NVIDIA + deprecated "nv" driver: no eyestrain, but at the same time no hardware acceleration
Maybe the Intel Iris Pro GPU has "better" drivers. I would love to test it, but a new CPU means new mainboard, new RAM, and, in my case, a new case + power supply unit. That is too much for just a test that might not be successful. When I have to upgrade my PC in the future, I might have a look at Intel GPUs.