What if a second lens needs adjusting? If Canon adjusts camera for one lens, will you lose its adjustment if you re-adjust the camera for a second lens?
Canon would adjust both the body and lens and adjust them toward the ideal setting. I had a 24L II that was out of focus. It was covered by the warranty, and I sent it in and Canon adjusted its focus. I got it back and it worked fine now. However the note they sent may stated that next time it might be better to send the body in too, so they can adjust both independently and together.
What I am trying to say is if your body is the one that has the tolerance error, then it might require all your lenses to have a AFMA of +15 for an example. If you got a new lens that needs a +8 adjustment on a neutral body, the closest you will be able to get is +20 (camera limit) but it needs a +23, so your perfect shots would be slightly OOF. If you send the camera in, then they can adjust it so that it is closer to zero, which would give you the full +/-20 range to make adjustments with.
You can check how well a lens' AF works by taking pictures with phase-detect AF and LiveView. A good lens would give you similar sharpness across the frame with either method. A bad lens might give you good LiveView performance, but be blurry with phase-detect AF. That is what I experienced with a 50mm f/1.4.