It's been that way for a long time, it's just kinda the accepted way. The vehicle builders had seen what garage door systems problems came about from hard-switched or dip-switched codes and just went that way from the start.
The newer vehicles have these always-on systems now, the owner doesn't have to press a specific button. So theives can amplify the fob signal that's constantly being emitted in the house and get the car to open, then program new keys once they're in the vehicle and drive away. But that has nothing to do with the Flipper, that's just a radio repeater.