I have migraines as does my husband. I am light sensitive. I also have glasses (quite a high prescription - higher than your son's, but was probably around that at his age).
I am bothered by light from overheard lights (fluorescent). If I go into certain stores that use very bright lights, I can only stay so long, before I feel totally drained. It's the same with some waiting rooms for example. It can 'trigger' a migraine for me. I leave before that happens. I know the signs. I feel totally weary. For my husband, he will turn the lights out in his office, otherwise he'll get those squiggles in his vision.
Your son may just be light sensitive - doesn't have to have a neurological condition (migraines, etc.). I don't know what kind of bulbs they use in his class, but a lot of people are bothered by fluorescent bulbs.
At work, people removed bulbs to make it a bit more dim - just over where they sat. So while you can't shut the lights off, they could control their own 'area' a tad.
The other option is the lens that dim slightly. You can have this adjusted to whatever you want. My sister has a pair that go from regular to total sunglasses for driving. However, they can be just slightly dimmed - barely noticeable. You would just talk to an optometrist to see if that's an option for your son. I know they cost more than regular lenses but if it helps with school may be good idea.
I think what I'd do first, is try seating him in different spots. It could just be 'glare' from the white board where it's light, and maybe away from a window, or whatever, or somewhere either further or nearer may help. Maybe he could go in at lunch and just work with the teachers until he finds a spot that lessens the effect. That would be where I would start. I know kids don't like doing that but it would be the simplest solution.
I'd mention it to his optometrist and his pediatrician though. I'd note if it happens any other time - like stores, or outside (bright sunshine) or if he ever comments from TV or using devices (screen time).
If it's just glare, then a lot of people get that - a lot of adults where sunglasses for that reason. He might need a prescription update and his eyes are just more tired than usual and he's responding to that. Is it time for one? I know if I wear my contacts too long for example (wear disposable) my eyes get really tired, drained, and are bothered by everything. Just a thought - if they are strained already, that would make it worse.
Good luck :) Hope you can find a solution