Is taking off the front black plastic cover around the shaft on the window motor considered modifying the motor itself?
Yes.
This also means that modifying the gearbox is considered modifying the motor.
Can you clarify which window motor you are talking about? Is it the Denso motor?
I’m not familiar with a black plastic cover on the Denso motor.
Maybe he means the spring clip?
As far as I can tell, you can only attach wires and remove pinions from motors.
Look closely at the regulation referenced above. It says you CAN modify output shafts, etc. The part in the blue box says, “Note that for the Window motors and the AndyMark gearmotor, the gearboxes are considered integral to the motor, thus the motor may not be used without the gearbox”, is just saying you can’t separate the motor and the gearbox". So you can modify the gearbox some, you just have to be sure it remains attached to the associated motor it came with.
It is integral to the motor, meaning that the only legal modifications are the ones listed in R49, there area a number of Q&A responses that support this.