Hi! First of all I'm happy to see there is a group of people trying to solve this problem. Most of the other threads are death leaving me without an answer.
So my situation is similar to all of yours. I can stay all the day on my Windows machine but 15 mins on any Linux distribution destroy my eyes.
Tried the pwn thing, different fonts, different desktop environments, different window servers, different hardware including graphic cards and monitors and always it's the same. From a old 2009 netbook to a gaming PC with and flicker free IPS monitor. I haven't managed to do the dithering thing on my actual PC since it's Intel graphics based.
Now there is something important that I think is neccesary to check and it is Android.
Android does not give me eyestrain on my phone and well uses Linux as a kernel!
Could it be something in the code of the Android graphic drivers that is missing in the PC Linux drivers?
I really hope we could find a solution to this. I want to come back to Linux but the eyestrain makes it an impossible task.