I recently got a OnePlus X. While the PWM of its AMOLED screen is pretty bad for my eyes, PWM turns off at brightness 81/255 and above, making the device perfectly usable. High brightness is not an issue. Even LineageOS (Android 7.1.2) is usable.
And on my OnePlus 3 I discovered that Paranoid Android (also known as "AOSPA"), a custom ROM, is usable. It has Android 7.1.2 and lacks the color profile options of OxygenOS (Android 7.1 and 8.0) and LineageOS (Android 7.1.2), which are totally unusable on any profile, including default. [Default was fine earlier on Cyanogenmod (Android 6.x) and OxygenOS (Android 7.0 and below).]
Which leads me to the assumption that something is wrong with how the color profiles are applied to the video output. Feels similar to the Firefox Quantum and Windows 10 post-1511 builds eye strain. I don't see anything flicker on a camera. Whatever it is, it causes eye strain reliably.
In summary: The OnePlus 3 so far had ROMS of Android 6, 7, and 8. Color profiles other than the default one always hurt. Then OnePlus changed something in their Android 7.1 ROM, so that the default color profile now hurts as well. LineageOS seems to have copied that change. The Paranoid Android developers obviously didn't bother at all to implement any color profiles, and the result is: no eye strain.
Maybe all of you who had trouble after upgrading their usable Android ROM had their video output changed in a similar way. If you are stuck on an older Android ROM and your device is supported by Paranoid Android, you may want to give it a try:
http://get.aospa.co