I have the mobo hooked-up to the car-alarm, and its just on for like 20 seconds and in the -10°C I already notice the difference.
but ya it could be done. the easy route would be if you know your car will be cold soaked when u come back just flip the switch before you get out.
the complicated way would be adding extra signals to your remote and having your remote starter controller know the difference somehow...
another thought would maybe instead of it being a switch, make it a relay that is controlled by a thermostat. this would obviously need a override switch but doesnt sound too complicated. hmmm. i might look into this (im sure its been done many times).
the biggest problem with my carpc in the cold is the screen. it is really unhappy and dim at temperatures where my hard drive etc is perfectly fine (ive never tried it below about 10F though so...)