audio: swap MOST system for aftermarket (MY03)?

[vr986]

Getting ready to buy a 2003 and know already will want to upgrade the stereo. Willing to go aftermarket (esp. with such goodies as iPod integration, bluetooth, and MP3 disc playback available; aware that Alpine and Nakamichi are common choices).

Have mined tons of forums like this one, spoken to a dealer and to a high-end car audio shop (in San Francisco), but have yet to come up with a definitive answer: will swapping out the entire audio system (CDR-23 head unit, and the stock amp in the front trunk if there is one) disable the factory alarm, or any other feature? (I'm not worried about the speakers for now.)

I understand the 2003's on up use the optical/MOST system for the stereo. It's just not clear if there's any other interaction tied in to this system.

Thanks in advance!