As a migraineur, that's the one thing I really don't like about flashing bike lights. It's just sometimes a bit close to the start of an aura for me when I see them.
Having said that, they're not generally in my vision for very long. If I'm in the car, then I will be past the cyclist in fairly short order. If I'm on the bike, then they will be way ahead and out of my view in very short order. So not really an issue.
I tend to use my lights on not-flashing, though, just because I know my eyes aren't fond of flashing lights.