Ok, power for locks, seats, headlights.. none of that goes through the pcm. Pretty sure we can rule it out. All this power and control of these various things does go through the BCM or body control module.

However...you appear to have a draw or other issue if you are finding the battery dead. I would double check that the the power cable from the alt is snug. Check the voltage etc of the battery, is it dead or is it just not supplying power to the car.