I do believe you were lied to by the dealer. I do not know of any changes to the speakers between ‘06 and ‘07 in the A4’s speakers. They are both B6’s with very little difference between them. If both had standard speakers, the loaner did not have Bose Premium Sound, there can only be a few differences.
Do your car and the loaner both have the same radio? Symphony II, RNS-E (Audi Nav Plus), etc. Different head units sound different. Have you adjusted your equalizer settings? Were you listening to the same thing? Over the air radio sounds worse than Sat. radio or a CD.

It is possible to upgrade, but be sure there is not an explanation for the difference before you spend the money. Bose speakers do sound better.

By the way, the new S8 and R8 both have Bang & Olufsen sound as an option, which sounds phenomenal.

Hey Michael,
Well, you said that the ‘07 did not have a tape deck, that would make it a different unit. That could be the difference in sound quality. Also I know that the head unit is no different on a Bose system, compared to a standard sound system. The head unit is merely coded to be Bose or Non-Bose. The Bose system uses active speakers with built in amplifiers. You could purchase Bose speakers and install them yourself. After installation, you would need to find someone with VAG-COM software, or take your car to an Audi dealer to have it coded. The radio needs to be “told” that it is connected to Bose speakers, to get the full Bose experience. Bose sound is tailored to the acoustic coutures of each Audi vehicle. The radio is already setup for Bose, but it needs to be coded. Installing Bose speakers would not be very hard nor expensive. I would not recommend putting aftermarket (non-Audi) speakers in your car, as they may actually sound worse. The impedance of both the speakers and head unit should match for the best quality.
I drive a 2004 Audi S4 with Bose, it sounds great.

Add a sub.