Originally posted by rodeknyt other than because of manufacturing slop, in which case one global adjustment would take care of it) and why would there be a difference from one lens to the next?
You have answered your own question. Manufacturing slop, or tolerances are not precise and vary from lens to lens (even in the same exact lens).
Modern cameras have three separate focusing systems:
1) The focusing screen, same as what you used in your ME Super, though not as good. Used for manual focusing. This can be adjusted by adding or subtracting shims above the actual focusing screen in the camera. Normally this is done in the factory and should be fairly precise but it can be off. And if you add a third party screen adjustment is sometimes needed to get what your eye sees in sync with what the lens is presenting to the sensor
2) PDAF this is the standard viewfinder AF system and out of the box is usually fairly good with slow lenses like the kit lens. But put a fast (f/2.8 or faster) lens on and the manufacturing tolerances may be enough to cause front or back focus. Not enough to be noticeable on a slow lens but easily seen on a fast one. As it was explained to me if both camera and lens are at technical zero then all is wonderful. But if the camera is off say -5 in one direction and the lens is off -5 in the opposite direction now you have a -10 error. That is why some lenses work fine on one camera but not on another. This system is adjusted using the camera's built in AF fine tuning controls
3) CDAF this is what is used in Live view and uses the sensor itself to determine the focus. As I understand it this is always correct and there is no adjustment mechanism provided. The downside, at least currently, is that this system is slower than the PDAF system though it is theoretically more accurate. Focus peaking on the Live View screen is the visual equivalent in CDAF of the old micro mirror prism screen on film cameras.
Hope that helps, and hope I got all the terms correct