The original post really had this one right, but a lot of the responses are off target, IMO.
The Fender so-called Custom Shop is really a very well tuned operation that produces some very excellent specific instruments, and will for a totally exorbitant price actually build a custom instrument.
The good thing is that they ARE producing excellent instruments dead center to what most Fender players really want, IME.
The not so good thing is that if a player wants a reasonably small tweak on any of the designs, the pricing pretty quickly doesn't make sense. Further, they won't even do certain tweaks because they need to keep their Artist series distinct; i.e. they simply won't do certain tweaks if they are features found on an Artist series. Just a small example is that I had a discussion with the Scottsdale office about building a Custom V with the 9" radius on the board a few months back; and that was completely rejected, as in would not even quote on it because that feature is found on the MM5.
So, they do produce some limited great instruments; but don't have actual custom work as part of the business model. I think you have to go from there, take it for what it is, and not get all excited about what it isn't; IMO.
For actual custom work, you've got Sadowsky, Lull, A-C, to name just a few. So, we're in pretty great shape for product availability/accessibility right now.
My 2c.