I just found this post on google and have identical symptoms as the original post describes.
I have been a lifelong windows user. I was issued a 2013 MBP retina through work years back in 2014, and used it without too many issues. I would get bad eye strain when it was plugged into an external monitor, which I attributed to the fact that OSX does hardcore font smoothing, so text is somewhat blurry at lower DPIs.
Due to that small amount of eye strain, I saw an optometrist who said I have perfect eyesight, but gave me a weak 0.25 prescription to help. Didn't help.
Work issued me a new 2016 MBP 15", and the eye strain is worse. I have a nice new 4k monitor (using macos and windows at "looks like 2560x1440"), but the monitor on macos only still gives me eye strain. It really makes me feel like I am going cross-eyed, almost. The panel on the laptop is not as bad, but still gives me a headache.
I've seen two more optometrists in the meantime who have also said my vision is fine, but gave me different prescriptions to try to reduce the eye strain. I'm up to +0.5 now, still 20/20 vision. The glasses hurt more than they help I think.
Still zero eye strain in windows with my desktop PC, my 2017 surface pro, or the yoga c940 I recently bought to see if that relieved anything. After putting the pieces together that the mac seems to be the issue, i've just been using my own personal windows computer for work instead.
I really just want to be able to use the mac, because I love the OS and the ecosystem (especially for my job), but I'm at a loss for what to do as well. Since I have issues with an external monitor that I also use in Windows, it has to be something at the OS level, I would think. I've tried all sorts of viewing distances and resolutions and such as well to no avail.
I guess this is not helpful since I don't have any answers, I just wanted to share my experience as well and maybe answer the "you need to see a doctor". Been there, done that, spent about $1000 on glasses so far.