Yes, they're physically different. I don't know if there are more menus but there are no more EQ controls. I don't know what is different about the Bluetooth setup but (a) it sounds better, much better, and (b) you get song titles on the screen. There is also Bluetooth FF/Rewind on the nav screen but it is hard to use so I don't use it.
For my $3,000 (tech package), not only did I get the Bose stereo, but I also got navigation, moonroof, power liftgate, fog lights, and satellite radio. That's $3,000 well spent in my mind. If it's true that you could build a better system for the same money, that's a shame that they didn't. But I consider it a great system, for the money and overall.
I agree that the EQ controls are totally lacking. I wish it would just have midrange; I would be satisfied with that. My biggest complaint with it overall is that it takes me one physical button and a whole bunch of touch screen touches to adjust the bass from high (music) to low (podcast). I would kill for a little knob like all the old OEM systems had. I can't do it while driving which sucks.
EDIT TO ADD: And the tech package also gives you advanced keyless entry, which is super duper duper important to me. I can't believe what a great deal that package is. Best $3,000 in the industry.