So why wouldn't they utilize it in their warranty program since it is less time consuming to 'fix' things this way? Not saying it's true because I have no evidence, just saying it is logical therefore entirely possible.
They wouldn't utilize it because then the user could easily 'unfix' the issue by turning off AFMA or by resetting the settings on the camera (which would not erase the adjustment, but would set the C.Fn back to the default 'no adjustment' setting).
People who've sent cameras and/or lenses in for adjustment have reported service reports stating, "Electrical adjustments were carried out on the AF assembly...," and for lenses, "The auto focus did not operate properly. Electrical adjustments were carried out on the circuit board..." That's not AFMA.
That assumes any service menu functioned identically to the user menu...which if such a thing existed I would assume it would not. It's easy enough to code to only flash the addresses you want upon reset and leave others alone so it has no technical barrier. And it is only logical to do this vs disassembly of lens and body simply for a lack of access to afma.
As for the service reports, I wouldn't be surprised if that language is used even on stuff they check out and is fine.
Again, no proof of this with Canon, just speculation based on how I've seen other places work where I do have proof.
I suppose if we had a single 60d and two copies of whatever lens with one off -8 afma units and the other off +8 and sent everything in we would have all the info we needed to definitively confirm or dismiss my speculations upon return of same.