The custom shop at Fender is there for a few reasons. Primarily, it's there so that, when a customer comes along and says "but I don't want on of the 3 colors you offer in your standard line", or some other simple variation on a standard Fender, they can make you want you want without shutting down the standard production line, and then they charge you extra for whatever it is that you want that's different. It also allows them to do non-standard things for high profile artists, so they can say that "bass player X" plays a Fender.
What people fail to realize is that "Custom Shop" is not really another step in quality. Sure, you can get rolled edges or something, but I can do that (I have) in 15 minutes, and for far less than they'd charge you to do it. The Custom shop exists primarily for Fender's convenience, and yes, it makes them a bit more profit per instrument than a normal one. But the parts they use are made from trees just like the stuff on the regular production line, and they're made in the same CNC machines, with the same programs. There isn't an identifiable thing that a custom shop instrument has the a regular production one doesn't, other than colors, how beat up it is, etc.
They've also figured out that people will pay for a bass that's "just like Jaco's" (or, in this case, Pino's). If that's you, fine, but always remember that that magic of Jaco or Pino doesn't come from the instrument. I could take Pino's exact instrument, he could take mine, and I'd sound exactly like me, and he like him - lucky for him the talent doesn't move with the bass.
My favorite "custom shop" instrument at present (for the irony) is the one that Gibson makes of Slash's Les Paul - it's a copy (naturally) of Slash's Les Paul, and it's made by Gibson. Well, if Slash's Les Paul has some magical qualities to it that normal Gibson Les Pauls don't, perhaps it's because Slash's Les Paul isn't a Gibson - it's a copy made by a small luthier. So, the Gibson tribute is their copy of someone elses's copy....of a Les Paul. Almost hurts my brain to get through that twist....