Thanks for your reply. I inspected the door and there is nothing at the bottom or in the track preventing it to go all the way down to rubber feet.
What I don't know is whether the motor is infinity motor and UP and DOWN stops are achieved due to resistance, or the motor has stops even if run disconnected from the regulator.
I watched a video on youtube, I think E46 rear window replacement and the motor had UP stop when running freely. But E53 motor is mounted to regulator prior to regulator installation.

So basically it doesn't matter in what position the regulator lifters are when mounting a motor, or is there some synchronization process like running motor freely all the way up (or down) until stop + turning the regulator manually all the way up (or down) and then mounting the motor to regulator?