It is true that a SC does have some parasytic drain on the engine, this drain is only when in boost though.
When out of boost the SC is effectivly freewheeling so has no noticable effect of the effiency of the engine.
Turbo's aren't exactly free either though.
Having that large blockage in the exhaust manifold does effect the efficiency of the engine and saps some power in the process.
Not as much as a SC granted, but then i've never heard of anyone going FI to improve fuel economy
the whine from a super charger can be annoying.
Few points here also.
1/ All the A3 3.2 SC kits i've seen offer a Rotrex SC, the Rotrex is a centrifugal supercharger so is basically a belt driven turbo, as such it makes no whine.
2/ The usual SC whine you refer to is usually from Roots or Positive displacement type SC's, even on these though the whine is only when the SC is in boost, so only a small fraction of the time spent driving.
3/ My MX5 has been supercharged for around 10 years now, even though 99% of the drives are with the top down so no sound proofing i can state without any doubt that i still can't get enough of that SC whine even after 10 years
SC v Turbo is a debate that's gone on for years, each has it's own advantages and disadvantages.
It's really up the individual to decide what will work best for them.
Personally i don't mind either way, i have a supercharged car, a turbo's car and a NA car, they all serve a purpose and they all do that job extremely well.
For the 3.2 i would personally prefer a SC over a turbo, simply because over here having a hot turbo, in a poorly ventilated closed in engine bay with very little room around it (a turbo is tight on a 3.2 A3) it tends to be a nightmare in traffic in summer (45c+ in the shade).
Out of boost SC's tend to run a lot cooler, so that's be my choice.
As i say though there is no right or wrong, if i found a well manufactured and designed turbo system for the right price, i could easily be swayed.