Fixing the built in garage door opener thing should be easy for the manufacturers. I mean, if you need a key to get in the car, then force the car to be placed in 'accessory' mode with the key before powering up the opener.
If it's a fob, force the system to require the fob to be present to allow the opener to work.
If it's a fob, force the system to require the fob to be present to allow the opener to work.