Don't see why it couldn't be done. Had a friend that used his Viper remote to roll windows up and down,turn on stereo and adjust the volume all while keeping the ability to control the alarm.
That is a feature of the vipers no? At least the nicer ones? I was looking at one that on a certain button press could start the car and lower the windows to a set height. Seemed excessive but neat in its own way.
MustangEvolution ROCKS MY SOCKS!!!