The problems of AF micro-adjustment are all mechanical/optical in practise, not software related.
Phase-detect AF works by comparing two images from either side of the lens, which is why it is much more dependent on a physically wide aperture than it is on bright light. It also operates within the zone of depth of focus rather than depth of field (as it must do) and while that is affected by f/number in the same way as depth of field, in terms of focal length they work completely opposite. Long lenses have lots of depth of focus, and wide angles have very little.
Assuming that the AF gets a decent lock on accurate focus, what it then does is instruct the lens to move by a certain amount. The accuracy of that movement is dependent on mechanical tolerances. At a given focal length and focusing distance, it is easily possible to get pretty much absolute accuracy every time. The problems arise when the lens has to move a different amount according to focal length and focusing distance, when a whole new set of mechanical tolerances apply each time - the lens has to move much further at closer range, and further at longer focal lengths too. So there are lots of permutations to cover, and lots of potential for error.
Which is why getting a zoom to be spot on at every possible setting is difficult, and why the lens is as critical to accurate AF as the camera. TBH I'm amazed that it is both as accurate and consistent as it is, in my experience.
On the other hand, contrast-detect AF (as in live view, and as in all these new mirrorless jobbies) doesn't suffer from any of these mechanical issues. In that sense, contrast-detect can never be anything but absolutely accurate every time, but the problem with that system is that it is both less reliable and slower at getting an accurate fix in the first place.
When those issues are sorted, and it's getting better all the time, contrast-detect will be brilliant. Imagine being able to lock on to a subject and track it accurately anywhere in the frame in real time
