Think the recess shoulder handles a lot of the torque, allowing the bolt to just have to hold gearbox in place. Without it the bolt is in shear (in a somewhat larger hole), tends to get loose, wallow out hole.
Having two out of three shoulders is probably ok as in the one on left side of your picture. Shorter bolt would prevent bolt rubbing or locking up the gear inside with a thinner gearbox case (more recessed as you put it).
What I'm interested in learning is if the motor driving gear to regulator driven gear alignment with the Porsche motor is the same as with the BMW motor or if it is offset, possibly leading to eventual problems. Guess I'll just order a Porsche motor and see.