Quote:

...Doesn't that assume the motor, frame and swing arm are perfectly aligned?...



It presumes that the axle is aligned with the swingarm pivot. It is possible that by doing it that way the front to rear wheel alignment might be off a little bit.

It is also possible that the wheels can be in the same plane but offset, & it is possible that the sprockets can be out of alignment although the swingarm pivot and axle are aligned.