You can see this in most LED car taillights if you move your eyes while paying attention to the light -- it will create a 'strobe' effect, a trail of images along the path that it traveled in your field of view.
Some people are sensitive to this flicker. A similar thing happens with most DLP projectors.
I agree that when viewed directly, it's quite unlikely anyone can perceive a switching frequency in the thousands of hertz. But if you sit in one of the closer seats, your eyes will be darting back and forth across the screen, which would be enough for that strobe effect to bother me if the frequency is anywhere near what is used in the taillights.
[1] https://www.thenakedscientists.com/forum/index.php?topic=451...
[1] https://electronics.stackexchange.com/questions/256336/does-...
PWM is done because it's cheap to implement given a fixed power rail and a digital control : need a single/couple of power switches that can even be integrated on die for low-ish power targets. continuous things usually need some kind of discrete filters, that means more components etc
http://www.eizoglobal.com/library/basics/eyestrain/index.htm...
I never tried them though.
Now I have a new (2017) MBP and I don't have any problem anymore, so I guess that they improved the technology somehow.
Looking up the retina displays, I see they are either IPS or OLED. The IPS likely has an LED backlight, and OLED is...LED. So a flicker is possible if they used PWM to limit the current to the LEDs.
Did you notice any change in the effect at different brightness levels?
I think the iWatch also has an OLED panel.
i have no eye strain from watching a projection.