I'm guessing that the Bose HU has speaker level outputs. This is getting fairly common in factory installed systems, eg VW. The HU has an integrated amp, so it can feed the speakers directly. Then for the 'premium' option, they just throw in an additional speaker-level input amp and change the speaker setup. Sometimes the HU is reprogrammed (it is in VW), but I believe this is simply to take into account the speaker changes (ie extend the bass range).
This allows the car manufacturers to only have to produce one model of HU, and gain cost savings in doing so. It will help maintain Signal-to-Noise ratios at the amp too - the radio frequency noise picked up by the HU->amp wiring is going to fairly constant, but the signal on those wires is much greater.

Certainly this would explain both of your symptoms. You should be able to find line level converters fairly easily, although it's probably a good idea to try and garner some opinions on various models before outlaying any cash.

http://www.crutchfield.com/S-XFoTipitu8G/cgi-bin/ProdView.asp?i=101PL2 will do the HU-->empeg part.
http://www.crutchfield.com/cgi-bin/S-XFoTipitu8G/ProdView.asp?a=0&s=0&cc=01&g=751&id=detailed_info&i=127OEM2 looks like it would do either connection.