Humm...I agree and have dealt with the same issues, especially if your work demands many hours in-front of the display.. continue to live with the eye & headache issues too, regardless of the monitor.
I thought the reflective mirror was also the cause (as with my beloved Apple Thunderbolt monitor). I also heard that Retina can cause eye strain and headaches to some too.
If what you say is the facts, then though Apple's Studio Display is quite expensive in comparison to it limitations and issues..but..."if" it does minimizes eye strain and headaches...then I would take a second consideration and look at it.
Hope to go somewhere and see the screen under the store's florescence lighting (as most stores have) to check the glare etc. Usually by looking at the screen for a few minutes, you can tell about eye strain etc.