I've got a retinal disorder that causes me intense, long-lasting afterimages from fairly dim lights (monitors, windows on cloudy days, etc). Brake lights don't bother me in the least, so I have no idea what you're going on about. I'd much rather know the car in front of me is stopped than have to guess that it might have its handbrake engaged.
Empirical evidence of the reactions of drivers behind me shows that they can get a clue. Or at the very least they get nervous that the car in front of them is slipping back, and they stop creeping forward clue or no.