It's all to do with the engine having to run at 60 frames per second. How long does it take for a ball to roll down a flipper? Less than a second, for sure. For the sake of argument, say it takes 1/10 of a second for the ball to roll down a flipper when it's released from a trap (I've not timed it and it's likely very wrong). That's 6 frames. So there are really only 6 possible positions the ball can be in when you flip.
Hmmm, that's pretty interesting. I certainly hadn't considered that either.
Still, the physics in Timeshock definitely feel more "wild." I would really love to know how they do it.