FWIW my background is in Mechanical Engineering. I know more than a little about how parts fit together and manufacturing tolerances, having designed Aircraft Components for 12 years. Here is my take on the bolt/neck pocket thing:
Fender basses traditionally have a relatively loose (by machining standards) fit between the neck and neck pocket. This means that the stability of the joint is determined by friction between the two parts. That connection is amazingly tight through the bass (in the direction of the bolts). However, it is not as tight rotationally and may be the reason for some misalignment of strings-neck-pickups-etc on those instruments. A tighter neck pocket IMO would have more to do with reducing misalignments and less to do with acoustic coupling. Once the neck finds it's place (under string tension etc) it shouldn't move. That may affect tone but maybe not like you think.
With the same tolerances and pre-set gap a 6 bolt neck would be better rotationally due to more friction and also the interaction of tolerances of six vs 4 or 3 bolts. If Fender spaced the 4 bolts further apart and lengthened the pocket, it would also improve alignments.
A precision sliding neck pocket joint may be a obvious design choice, and not a problem for CNC machines at all, but will have other repercussions in manufacturing due to different expansion/contraction characteristics of wood types and grain directions. In other words they may make perfect parts today and half of them won't fit next week when the humidity changes. I'm not saying that the pocket can't be tighter than it is, it's just that the mass manufacturing (in several locations) that a company like Fender does kinda forces them to make every neck fit every body. Making a substantially tighter fit would increase the hand work required to sort and fit parts together. I would like to see it but that would affect their bottom line.
IMO if you are interested in maximum coupling and alignment perfection, you need to look at set necks and neck-thru designs or go to a smaller maker who is willing to fit each neck to it's body. Obviously guys like Mike Tobias do a great job with that.