I don't think you are correct on the whole scene having to be redrawn. Maybe that's what those engines do ... maybe it depends on the type of structure the alpha is applied to. I can see that with TSE currently ... it seems to be able to drawn an 'alpha'd' component separately whereever it wants on the screen. I've noticed some strange occurances because of this ... but honestly I don't know what's going on behind the scenes. I would think the hardware at this point is designed for many alpha transparency effects in mind. I've certainly seen no shortage of it in current games.
Additionally, maybe the game's running at 1,000 fps without alpha effects?
Additionally, maybe the game's running at 1,000 fps without alpha effects?