I wouldn't even use a heat pack for the longer drive. The travel container is in YOUR possession and YOUR control. You control how warm your car is. There's no reason to expect it to be less than comfortable for the entire drive. Even if you stop for gas and a snack along the way, the temperatures inside an insulated container will not change much, if at all. On the other hand putting a heat pack INTO an insulated container that is IN a warm vehicle is asking for trouble. The inside of the container could get far too warm.
If you're really nervous about the longer trip, I would suggest carrying a heat pack with you, but don't activate it unless there is some kind of emergency along the way and the snakes might have to spend several HOURS setting in extremely cold temperatures. The few minutes it takes to get to the car and warm the car up won't affect the animals at all, so long as they are well packed and insulated, just as you described for your shorter trip. :)