I have both a roof rack and a garage. My solution to this problem is that when I put bikes on top, the door opener goes somewhere that can't be reached without getting out of the car (usually all the way in back so I have to open the hatch).

Roof racks are very convenient if you carry bikes frequently and don't want to block access to the back of your car (some rear racks don't block the back). Mine is also much more solid than any rear rack I've tried. You just have to be aware of the standard mistake that people make and make it harder to forget they're there.