AF Micro Adjustment 5D2 to 5D3
That would be an incorrect conclusion. Microadjustment does in fact affect lens-and-body as one. Now it may very well have been the case where you find yourself with an old 5D2 and a new 5D3 to be of similar build tolerance, in which case the MA offset would attribute mostly (or entirely) to the lens intolerance. That is actually a good thing and merely demonstrates Canon doing it's job right -- making ALL cameras to their intended tolerance (ideally @0).