I test all my lenses at 25x and 50x the focal length (and I also tested the 100L Macro near the MFD with the small FoCal target).
Rick, you say test wider than f/2.8 - do you mean narrower? Lenses should be tested wide open, f/1.4 in this case (which is wider than f/2.8). Wide open gives the thinnest possible DoF for the test, which should mean more accuracy. Normal AF is always done with the lens wide open.
If a narrower aperture shows backfocus, that indicates the lens has focus shift (e.g., the 50/1.2L). In that case, you can actually use AFMA to compensate for the focus shift. Not really 'on the fly', but if you're shooting a series of shots at the same aperture (say, f/1.6 on the 50L) and subject distance, and you have determined the AFMA for those conditions (which would be different than the f/1.2 AFMA with a close subject).