However, I think what you need to factor in to the analysis and what many folks don't seem to consider is that the bike in your head and the bike you walk out the builder's shop will likely not be the same. How close you get depends on a lot of things. You suggestion to go to a builder who has loads of experience building the type bike you want is a good one.
In the most recent article of Bicycle Quarterly, Jan Heine wrote an article that basically said the same thing.
You can go to a custom builder with a lot of experience building a certain kind of bike and ask him "build me one like that," and get a bike "like" his past work, maybe with a few tweaks. But if you go true "custom" - something really unique - almost by definition you're getting something so "custom" that you're almost getting a prototype (esp. if the builder doesn't have years of experience).
He ended up suggesting (I think seriously) that if you want something really unique you might have to get two frames -- work with the builder to build your "dream" bike, but don't spend money painting it or doing anything fancy. Ride it enough to know what needs to change, and then have a second frame built that "fixes" anything wrong with the first one.
I am not advocating or defending the point of view, just passing along another caution about custom bikes.
(BTW, I have a custom bike, and love it).