I am sorry if I implied that, but that was not my intention. My perspective is from the software side, not the mechanical side. I agree with both of you. The AF system operations, adds the offset, then the mechanics happen.
However though, there might be a difference with the closed loop AF that exists with some of Canon's lenses. There are some newer versions where there are some back and forth between the lens and body, and AFMA may operate a bit differently there, ie. "I calculate where to move, then you the lens moves and tell me when you are done and in what position you are, and I might readjust". This might only be in AI servo though, I am not sure, we never received clarification about the improved AF closed-loop communications.
Most lenses however operate under this "I calculate everything, then tell you the lens to do something, and I expect you to comply". The lack of a secondary review of how the image now looks after AF occurs is one of the reasons we have AFMA, the tolerances of the sensor and lens positioning of the focusing lens group can often be off.
This is where Sigma lenses, where you can make 16 different adjustments within the lens firmware, starts to cause some issues. Obviously if you go to that level of AFMA, then you most likely don't use the in-camera version. The lens now sees what the camera sent it, then it runs through its 4x4 grid of AFMA values and decides what to apply to that position, then moves the lens focusing accordingly.