Well, thats what the timers on the shut down controller are for. You could easily have it set to shut down after say a half hour after the ignition has been turned off. This would give ya plenty of time to stop and get gas, or stop at the store to pick something up. This would also not be a problem with running the battery dead on the car, as a half hour is no problem.
Also with the remote start (I spent a bit of extra money for that when I had the alarm installed) I want the ability when I am getting ready to leave the house, to start the car with the remote like 10 minutes before I leave or so. This will give the puter it plenty of time to boot up, and then sync to get the latest weather, traffic and such by the time I get to the car.
The same works when coming out of a store, I start the car when I walk out of a store, to get the A/C going and the puter booted up by the time I get to the car.