The thing about bolt-on necks is they're manually put on. To put one on and expect it to be perfectly aligned every time is dreaming. I don't care if it's cnc or not. And some guitars have shallower horns in the pocket location making for a less stable coupling, and there are those that may even have looser fitting pockets. Yes, they should make sure and align properly at the factory -- but it's not totally uncommon for a bolt-on to shift in the pocket over some time either. Unfortunately with set or neck-thru designs you're at the mercy of bridge and nut alignment.
