Well, my D800 had this kind of issue where many of my fast primes required a different AF fine tune setting to get good results for different distances, this was a major pain. Nikon adjusted the camera and that didn't affect this characteristic. I then later on moved to D810 and this problem is largely absent now, as is the problem of wavelength dependent AF error. This latter Nikon actually acknowledges and advertises having been fixed in the D810 and the newly announced cameras.
I don't know what the cause of the problem was but it was not a small effect, it was considerable. Since it occurred on several lenses and seemed particular to one camera I didn't take the lenses in. However, I think this is something Nikon should sort out internally; it gets very complicated if you have to do AF fine tune settings for different focal lengths (the effect many not be linear between wide and tele ends of a zoom) and distance.
I find that in the lenses I've purchased in the last few years and newer bodies there are fewer problems and focus problems seemed to peak at 2004 (D70, yikes!) and 2011-2 (D7000, D800) and nowadays my kit works very nicely, even though I still have to fine tune some of my fast lenses. I'm happy to see some automation in the latest bodies for fine tuning.