Is that a proper "fix" though? Manual says to avoid MF adjustments unless absolutely necessary. Seems odd that a new body would be incompatible with so many lenses... no?
"Avoid MF adjustments unless absolutely necessary," doesn't mean don't do them at all. The feature is there for a reason. Looking at your image of the 50/1.8 box, I'd say that an adjustment was
absolutely necessary.
If you're waiting for a magical, "tried and true 5D mkII," you might be disappointed. I have both a 7D and a 5DII, and my AFMA results are below.
I've calibrated 14 lenses on my 7D, and 13 of them have had some amount of adjustment applied. Obviously, the amount of AF microadjustment needed will be different for each unique camera and lens combo, so these numbers are useless to anyone else, but to give you an idea here they are:
–5 EF-S 10-22mm f/3.5-4.5 USM
+9 EF 16-35mm f/2.8L II USM
+1 EF-S 17-55mm f/2.8 IS USM
+2 EF 24-105mm f/4L IS USM
+2 EF 70-200mm f/2.8L IS II USM
+6 EF 70-200mm f/2.8L IS II USM + 1.4x
–7 EF 70-300mm f/4.5-5.6 DO IS USM
–3 EF 85mm f/1.2L II USM
±0 EF 85mm f/1.8 USM
–1 EF 100-400mm f/4.5-5.6L IS USM
–1 EF 100mm f/2.8L Macro IS USM
+5 EF 135mm f/2L USM
–2 EF 200mm f/2.8L II USM
+2 EF 300mm f/4L IS USM
On my 5DII, I've calibrated 8 lenses and all of them have needed some adjustment:
+5 EF 16-35mm f/2.8L II USM
+6 EF 24-105mm f/4L IS USM
–1 EF 35mm f/1.4L USM
–3 EF 70-200mm f/2.8L IS II USM
+4 EF 70-200mm f/2.8L IS II USM + 1.4x
+5 EF 85mm f/1.2L II USM
+5 EF 100mm f/2.8L Macro IS USM
+3 EF 135mm f/2L USM
An adjustment of up to ±2 would probably not be 'absolutely necessary' in most situations. But, an adjustment of ±4 means that the lens+body combo is off by approximately 1/2 the depth of field for shots at a 'normal' distance (i.e. not close to the MFD or infinity) - that's enough to be noticeable in typical shooting, at least for me.
I use the
LensAlign to do my AF microadjustment calibrations (I use the Pro version, which is no longer available; the MkII version is an update to the also-discontinued LensAlign Lite that incorporates the important features of the Pro version).