I don't know about the new Bose systems, but both of my 1st gen Mazda 6's had Bose systems in them and they both had one or two adjustment potentiometers on the amp under the front seat. Needed a small screwdriver to adjust them. Some people reported some success with tweaking settings on that, but I don't recall if that only controlled the subwoofer or all of the speakers.
Another feature that can affect sound quality, too, is the ALC settings. Using a high ALC level setting can cause the speakers to start distorting.
Also, who knows what other people fiddled with when taking test drives or looking on the showroom floor. It's entirely possible the car you got had been sat in by other shoppers and had the radio settings tinkered with to intentionally make it sound bad to see how far they can push it before it starts to sound like crap. Like cranking both the treble and bass and ALC settings all the way up and/or screwing with the balance/fade. That's a recipe for making almost any factory sound system sound like garbage.