The adaptor plates for the A3 actually screw in either side of the dash aperture (or at least the Autoleads ones we sell do anyway), and should work OK with the Empeg cage. The only slight problem you might encounter is that the Empeg cage tends to be just a little bit under standard DIN size (probably only by 1 or 2mm), and you may find it's a bit loose in the dash. If so, it ought to be simple enough to remedy with a thin plastic or similar shim.
All the Bose systems in A3s that I've seen have used the head unit's inbuilt amp to run the front speakers, and the slightly odd level pre-amp output from the unit to drive an active amp in the rear. We sell an adaptor lead for these (again, it's an Autoleads part) that allows you to run a 2v+ pre-amp output into the original amps. This ought to work fine with the Empeg's higher than average pre-out voltage, so all you'd need to add is a small amp to drive the front end.
The Bose systems do tend to sound pretty good - we'd be hard pushed to offer an equally good system for the same price, and it wouldn't integrate quite as neatly into the vehicle. It pains me to have to admit that, but manufacturers in general (and Audi in particular) have actually got their act together a bit better of late.
Dominic
Cambridge Car Audio
http://www.cambscaraudio.co.uk