Yeah, I see your point, I guess it's one thing getting it to work with the adapter, but another whether it sounds any good. According to the guy on the Audiworld tech site, he spent weeks with his Bose system in pieces and ended up putting it all back as was. He very strongly recommended that you leave as is, or change everything.
The Bose system is radically different from the non Bose system. It uses an external amp to drive all six door speakers, which are 2 ohms each, not 4 ohms, so you can't easily by pass it. The Bose sub is driven by it's own 100watt amp inside the sub enclosure. I think if you are happy with the Bose setup then the adapter should work fine (albeit subject to Audi's noddy wiring looms). I think problems arise when you want more power, and want to by pass the Bose amps. You then have to change the speakers, which you'd probably want to do anyway as part of the upgrade. I'm now wondering if the Bose sub runs off a connection from the other Bose amp rather than the HU. This could be why I'm getting the wierd "pops". I think I'll stick with the Alpine amp setup. If anyones interested, here's the latest development in the A3 sub experiment. Now I'm a dad, my wifes Alpine ported sub has had to go up in the loft to free up boot space in her A3T. So I bought a Bose sub in the laughable hope that it would give something approaching bass in the now subless A3. It was an improvement, but disappointingly used the same flimsy tupperware enclosure of the standard unit and even with extensive Dynamatting hardly provides a solid base for a sub. So I set about making a new enclosure from MDF. And here it is. I managed to make it about 2 inches bigger all round than the standard unit, by reorganising the wiring behind the standard unit. The improvement is dramatic, but now looking to shoehorn an 8" driver in there, as the poor little Bose drivers are struggling. I'll keep you posted: