I have a theory as to why they can't fix it with simple adjustments and calibration. See the following image.
Supposedly there is some internal calibration of all of the individual AF points. If the warping of the AF module is too extreme such that it can not be adjusted electronically, then replacement might be the only option.
Or it could be very difficult/costly to reprogram the module's calibration table. The table may be stored inside the AF module itself and hard to get at without complete dis-assembly of the camera, or burned into some kind of ROM at the factory. It could be that the AF module is calibrated to itself outside of the camera before it's installed in the camera. I don't have sufficient knowledge of the camera's internal parts to know one way or the other.
These are suppositions on my part, but since Nikon won't comment and I haven't personally seen a resolution to the issue, what else can I do?