Tbh I think you've probably summed up everything I wanted to know about it, in that its not plug n play. The pops are enough to put me off it, although it'd be interesting to see how it behaved with an aftermarket amp as I have had other aftermarket head units pop and click with Audi amps.
I wonder if the supplier would send out an eval unit for more tinkering? I've found a very nice Kenwood amp which fits in the stock Bose location, although it would probably turn the stock Bose speakers in to molten slag