I agree with the goldwing2000's sentiment about there being cpu circuits controlling who knows what. Kinda reminds me of the older civic (late ninety's) where you had to keep the stock head unit in the dash to retain door locks or domelamp or something. You had to intall a Y adapter for some of the wires to route power to the stock and aftermarket HU and then stuff the stock HU behind the heater control area to make room for the new HU.
However, in the 3, there is nothing about the factory deck that controls anything else other than audio. As long as you're careful about where you drill holes and run wires (and don't yank/stretch/stress other wires when you run the new wiring), you'll be fine. Stick to the "accepted" methods of stereo installs and there will be no problems. Once you start adding things like remote starters/alarms/window roll modules/etc do things get more involved because you start tapping into things CPU controlled.
BTW: Speaking from experience, basic alarms with door locks, door/trunk triggers, and flashing parking lights are easily installed in the 3.
