You're right "it finds its own reference point" meaning one where it sense some mecanical resistance, with a broken mount it may be some other point of the mount than the regular stop or worst if the mount is completely broke it may be flap resistance when it reach it's full close or full open position... worst because the step motor torque is high enough to break the flap itself (for ex: make the shaft molded within the flap to spin freely inside of it) something you would like to avoid. As you see the stops (fully close and fully open) on the step motor mount are a MUST to reproduce when you build a new mount.
When you'll pull out the flap rod of the step motor arm you will manually and easily discover the fully close and fully open position of the flap (if the flap is in good shape) so this will give you an idea of how many degres the motor have to rotate from extreme positions, so where to put the stops on your new mount. When you activate the step motor (SM) in your rebuild mount if the SM arm does not fall within the two stop zone it's easy with a good plier to bring it there, the SM have relatively high torque but you could force it's arm where you want.
An other point: Your rebuild mount will never be to sturdy ! Remember, the SM have high torque, that's why overtime a weaken mount broke, so if you want it to do the job properly the first time make it unbreakable !