Tiny amounts of error in alignment are very unlikely to be audible, let alone the sole cause of gross misbehavior of the cartridge, e.g., skipping. I suppose gross over- or under-estimates of AS could do that, but the cruel fact is there is no absolute correct value for AS, because the skating force varies across the LP surface, from outer grooves to inner. So most of us seek a happy medium that does not result in a deviated cantilever or "skipping" or other forms of misbehavior that we ascribe to the skating force issue. It's not that hard to get there. I take issue with what daveyf wrote in comparing MM cartridges to MC cartridges, implying that the latter require a rocket scientist for maintenance. The skating force will be related to VTF, stylus shape (as it affects the size of the contact patches), and the moment of inertia of the tonearm/cartridge assembly. These all affect friction between stylus and groove, and friction does not know or care whether the cartridge is an MM, MC, or MI type, albeit we do find the more exotic stylus shapes on latter day MC or MI types, mostly.
So, all of this said, I am beginning to wonder whether there is an occult problem with the OP's tonearm related to bearing friction or the like.