No one knows for certain what Nikon does during the repair - or if they always do it. They may analyze the fault first and then the technician decides a course of action. If the technician decides to simply move the mirror or AF module forward or backward, and NOT re-calibrate the individual points then problems may persist.
Additionally, there is no first hand proof that they even have the ability to do this. Sure, we have several bloggers repeating what Nikon representatives have told them in private, but no official statement from the company.
The other possibility is that the AF module, mirrors, or assemblies are bent to an extreme that they simply cannot be adjusted for in any calibration, i.e. the calibration values are maxed out.
Let's say for the sake of argument that each focus point has an internal adjustment of +/- 10 and each step is a 1 thousandth of an inch. Now, lets say that all values are typically at or near 0. Maybe the AF modules are deflect by 0.015 of an inch, so all of the internal focus points on the left side have been maxed out at +10. This would be insufficient to correct it. However, if the technician were adept enough to set all of the other points to -5, and then offset the mirror mechanically by +5, this would yield a better result over all.
This is all speculation, it's just a theory of mine.
As for the use of AF-S lenses... You may be right, maybe an AF-S lens would work. I think you are implying that AF-S lenses are more accurate than screw-type focus lenses. I think this is completely bunk, and the reason is, the focus drive mechanism is just the output of the AF system and the CDAF (live view) system is fully capable of controlling screw-type focus lenses into perfect focus every time. It also doesn't help that my D300 can focus this lens using the PDAF system with no trouble at all.