I don't think there is a rule saying you can't. You probably can. But if I were you, I'd definitely include a warning/disclaimer. Of course, what you're gonna be dealing with is a "seizure warning". https://en.wikipedia.org/wiki/Template:Seizure_warning (This is not legal advice, obviously)
I would also include it on the itch.io page when you have a playable build, so people prone to seizures know not to bother downloading it.
If at all possible, I'd suggest you have a way to turn off strobe effects in the menu, and add a message that says "turning this off is not how this game is intended to be played, but this option to turn it off is provided for X reason". Or something like that.