[John]

"output shaft interface" typically refers to the external part of the gearbox, where you would mount a sprocket or a driveshaft.

In the past, this rule has been present in basically this exact same form. Every year, removing the window motors has been illegal.

Looking on Q & A, a team has asked about removing the gearboxes from the AndyMark gearboxes. Since this is not one of the listed ways you can legally modify a motor, FIRST directed them to R49. I would expect the same to apply to van door motors.

That said, any answer you get here is not an official answer and cannot be used to prove whether a design is legal or illegal. So you may want to ask Q&A anyway, though you probably don't want to count on being able to use your design.