As a sound engineer, I'd like to chime in on the quality of the CX5 Bose system. I took an extended listen at the dealer with "Off the Wall" by Michael Jackson and "Ten Summoner's Tales" by Sting. From my past experience, Infinity, Polk, and Alpine have the edge. I have a custom Infinity Reference system in my current car, and it sounds tight, transparent, and balanced. I was skeptical of Bose, because they notoriously use their name to overvalue the actual quality of their product.
This was not exactly the case with the CX5 Bose system. It sounded good, with a sound that really filled the cabin evenly and was well articulated. In my mind, it scored something like a "B-". I believe that for the meager price increase ($600 or so), the system is definitely worth it. You could easily spend $600 on a (marginally) better aftermarket install, but only if you bought speakers on eBay and did the install yourself. When you factor in the time, effort, margin for error, and decreased resale value, it really makes sense to go with the the factory Bose system - especially if you're also in the market for a moonroof.
The audio controls were not very robust. Basically, you get volume, pan (left to right), fade (front to rear), bass, treble, and Centerpoint. From my understanding, the Centerpoint system essentially adds short digital time delays and small volume adjustments to each speaker, resulting in the sound from all 9 (?) speakers arriving at the driver's ears simultaneously, thus "centering" the perceived sound at the driver position. This seemed to work fairly well, but aftermarket headunits allow for greater fine-tuning in this department.
I don't believe the CX5 has the trunk-mounted subwoofer that is included with the Mazda 3. At least I couldn't hear anything that sounded like a sub or had as much bass as the Mazda 3 Bose system did. I was also disappointed at the lack of a "mid" EQ adjustment, as I found it difficult to use only treble and bass to adjust.
All in all however, I'm sure that even critical listeners would be impressed enough to find value in the Bose package. The treble was distinctly clear - something you would expect from a good custom system. The sub frequencies lacked, and the high-mids were a bit prevalent and thus harsh. The speakers sounded tight, hinting that the speaker cones are at least not made of paper.