plenty of people do this, im getting ready to do the pi swap very soon. the only problem with supercharging a pi swaped motor is:
1. your compression will go up after the swap, so you wont be able to run alot of boost
2. if your car is old enough to do a pi swap on, chances are the motor has quite a few miles on it and a supercharger will just increase your chances of pre-mature engine failure.
if i was going to throw money into a motor with something like a supercharger, i would go ahead and do the full engine build with forged internals and ported heads and whatnot. thats why im only doing the head and intake swap, then im stopping from there.
out of the mustang game, got me a lightning