I agree that having the same builder for CS would be fun and interesting but there are so many options that it wouldn't be easy to build. And then when people started to see the price, another thread would be opened titled "Fender wants $$$$$$ for that? Ridiculous!"
That's kinda happening now anyway. But the whole point of a custom shop is that you pay extra to get exactly what you want. Who cares if it's harder to build? That's why they charge the extra.
Not to belabor the point, but that's why I like Warmoth as much as I do. You can get exactly the part you want with exactly the options you want, for a heckuva lot less than what Fender would charge for the same thing. Want an alder body with flame maple top, and a birdseye maple neck with an ebony fretboard? Done! Mahogany body with figured bubinga top and pinstriping? No problem. Want stainless steel frets? Gold frets? No frets? No problem. How about turquoise block inlays? Shark fin inlays? Gothic cross inlays?
I could go on, but you get the point. My three-pickup Jazz body is a Warmoth custom creation (I got the bubinga neck with wenge fretboard from the showroom, so it wasn't exactly custom -- but try getting one of those from Fender!). Getting the pickup routes exactly how I wanted them cost me an extra $90. And since Warmoth is licensed by Fender, there's no worry about compatibility.
Now granted, a Warmoth bass is a bit more DIY than many people might like to deal with. But the easy solution to that is get everything you want to go on your bass, and then take it to a tech and have them build it for you. In my case, I installed the shielding, bridge, and pickups. I had [Invalid or Expired Link Removed] do the electronics, and then I had [Invalid or Expired Link Removed] install the tuners on the neck & the neck on the bass using machine screw inserts, set it up and PLEK it.
And all of that cost me about the same as a "custom" American Design Experience bass would cost me. I'm pretty sure I couldn't even get my bass from the Fender Custom Shop with my wood choices -- but if I could, it would probably cost me about twice as much as the bass I got from Warmoth.