Are we the problem? Is it really our eyes or brains that are "messing up"?
It could be we just have superior visual processing in one way or another.
Those of us sensitive to PWM - it could be we just process visual information faster than other people. Look at all those who don't notice the flicker of an incandescent bulb. Incandescent doesn't cause me pain but I can always tell it's not a steady light most people don't notice this and you have to go out of your way to show them and even then a lot of the time they'll be like "I don't see it". I assume this would be the same reason some of us think we're sensitive to dithering. Generally "normal" people will get the same symptoms as us if the PWM is too low for them albeit at a much lower frequency.
Same with if it's the frequency of light maybe we're just more sensitive to it. There are people who can see UV light, people who see a lot more colours, what if we're just seeing something most people aren't and LEDs are producing it in too high of a quantity for us to be comfortable?
What I'm saying is, we're all looking inside but what if it's not us that's the problem but every body else?
Of course we should be looking at ourselves and trying to figure out if there's something wrong with us that's a problem. However, it could be just our eyes/brain aren't wired right or high rates of flickering causes something akin to a seizure - In some ways it does make me think of epilepsy.
I think the easiest fix would be finding out the true outer cause (the problem with LEDs, the problem with drivers, PWM) to our problems so we can come up with a real work around. Most of us (or all) are not all that sure what our issues are actually caused by just that some things hurt and we do not know exactly why.
It could actually be a defect we have but could it not also just be that we're just better at visual processing in some way?