The shop always has the final say. Though if you kind of know the rough boundaries you can sometimes work a few places to stretch things, and I never ever want to be a jerk about things. Once I did push back on something and someone up the ladder put a kind word in for me though. In this case, if the volume and tone control are 'stock' pots they're pretty easy to switch out for push/pulls I think.
My Z1 was an exercise in 'let's do most of the options and some that aren't options.' but it was a different day and age at the shop and it was builds like mine that helped put the shop in precarious shape for a while...I understand that and understand why a bunch of the options on that bass no longer exist. To that though, Sheldon also invented some options to try out on my bass. They didn't all work but it was fun to field the ideas of someone who was so creative both artistically and in terms of engineering.
This P is less that. It's the recreation of the bass that my subconscious has latched onto and shown me. That bass was pretty no-frills and I dictated it out of my dreams. Rather than most other 'custom' builds where people labor for hours and weeks and months over details...this was not that, and this bass isn't intended to be that kind of tour-de-force of all-outness. I'd rather have it be a stripped down sledge-hammer of an instrument, how my old P-Bass was (I once took it to a yardie jam in a bad neighborhood based upon the idea that it would be the best bass to hit someone with and still have it and me survive with maximum damage).
...and besides the switching happening today my wife (who's good at keeping her ear to the ground) said "so...I hear you've put a deposit on a new bass...I guess you've got a year or two to save your pennies for the rest of it" so that went fairly well.