To run a Custom Shop like Fender or Gibson says a lot about how little confidence they have in their regular line. And I can kinda see it - Gibson are miles better than they used to be, but their whole "close enough" mentality isn't good enough for the prices that people are expected to pay. And Fender USA still can't route a neck pocket that snugly holds a neck.
So what value do these "Custom" Shops provide? In Gibson's case, you ARE getting a better instrument, albeit for outrageous used car prices. In Fender's case, there's just no argument -- a FSO is an instrument designed to be easy to manufacture on an assembly line by unskilled workers. The whole point of a better Fender is self-refuting because of the way that Leo designed them - they're all meant to be inherently good because there's very little that you can screw up on them. Except, apparently, the neck pockets.
And the Custom Shop response that the necks aren't easily replaceable on an instrument designed to have an easily replaceable neck goes beyond the pale.