Bit late to this, but it's a real interesting thread.
My first reaction to your original post, which hasn't changed while reading, is that I might possibly be a luthier's dream ... (except, at the moment, I won't spend that much on a single guitar!! :lol:)
Personally, I'm after an instrument, not a piece of furniture.
That's not to say that I disagree with other folks who want their perfection on an expensive jobbie, it's just that I don't view it in quite the same light.
I've yet to spend over a grand on a guitar. The most expensive one was just under, and it has some serious "who the f*** was doing this fretboard?!" eccentricities (it's a Gibson :D). But the thing is, it plays and sings like a dream, and even if you were watching me from the front row, only I would know about the scratches and dents in the fretboard.
I saw all these issues when I was evaluating it, and I was surprised by the "workmanship" that got through, and was even worried that my wife, who was with me, might see the marks and think it was a bit naff for the price of the thing... but it was absolutely obvious it that was a stunning guitar in my hands (to me and to her), and it would have been foolish to pass the thing up because of some marks that didn't really affect its worth, to me, as an instrument...
Now, if I came to one of you guys to build me a beast, I know that you probably wouldn't even let me see a fretboard like this particular one - if it went like that, you'd curse yourself or whoever had done it, and put it right. Conceivably, if it had happened near the end, and fixing it could drastically change the nature of the instrument, which was already proven - I'd imagine you'd want to consult with me along the lines of "look, this has happened, we got some options, one of which is fixing it, but the sound/feel might change..."
If I was going for custom build, I'd be hoping for the "instrument" bits of it to be glorious (the feel and playability, etc), and the cosmetics of it to be "pleasing". I'd have already checked out the builder's work, and would have some idea of the standard to expect. I'm not into flashy finishes, or at least, not that much, so I'd be speccing up a guitar that cut that side of the cost down to obtain an instrument that felt and played like a million dollars for as cheap as could be managed.
So for me, I'd want to spend on the guitar, and pay the minimum for the cosmetic perfection (knowing that most of you guys are going to take a fair bit of care over how it ends up anyway :D)
... Hope that helps :D