Thanks, Greg. Although I'm sure this is impossible, it would be *very* interesting to see side-by-side the "same bass" made via the option order pathway and via the custom shop pathway. What's your impression of the custom shop product so far?
I've had two Custom Shop instruments come through the store, one guitar and one bass. I can't speak very well to how the guitar turned out (all guitars feel like junk to my hands), but my customer was very happy with it. The bass came through just last week, and it was awesome. The main differences are one subtle one and one not so subtle one. The subtle one is the finish which is a thin skin urethane, so there's a bit less material coating the wood and (theoretically) damping it. Could one A/B two basses and pick out the one with the thin finish? Possibly, I guess. The not-so-subtle difference is the hardshell case. It's a little more plush than the typical USA made hardshell case, and comes with a big embroidered "G&L Custom Shop" logo on the inside. It's a lovely thing that reminds you that you splurged every time you open the case.
Don't quote me, but the typical Custom Shop instrument will come in something like $600-800 more than an apples-to-apples Option Order instrument. That said, there are some options available on Custom Shop instruments that are NOT available on the Option Order ones. Handwound pickups available in various windings, different woods, etc.
Another key selling point is that there is one guy dedicated to your build start to finish, and he's on top of all of the details. If you want a piece of Ash with a certain grain pattern or a certain weight, he'll make it happen by painstakingly poking through the wood pile. We had a neat experience with the Custom Shop guitar that was made for us. Digging around looking for the neck wood, the custom shop guy found an amazing flame maple neck that had a similar neck profile to what my customer had ordered. The neck was mostly carved and very nearly done. I got a call from the custom shop guy mentioning the neck, I passed the info along to my customer... and he ended with an incredible flame maple neck at no upcharge. That was really nice. Obviously, I can't promise that something like that will happen with every build, but it's the kind of thing that is possible with the custom shop guy paying that much attention.
The main drawback to the custom shop is the build time. A typical Option Order G&L gets done in less than 10 weeks, and 6-8 weeks is pretty typical. The Custom Shop builds have both taken 6 months. I assume most of that time is spent just waiting for the custom shop guy to get done with prior orders so he can focus on your thing. So it's probably more a backorder thing than him sitting there whittling the body and neck with a pocket knife for 6 months.

My impression is that he handles the wood selection part very carefully, then he turns the wood over to factory for milling and painting. Once the pieces are completed, then I assume the custom shop guy gets involved again in final assembly and setup.