Well, I'm sure I'm not the most appropriate person to talk about this as I have no interest in custom or exotic woods but for I've read, and maybe I'm completely wrong, custom builders use to hand build the whole instrument or at least a big percentage of it. And that is what IMO makes a custom build an expensive build like building a classic Rolls-Royce Phantom II when workers cut, shape and finish almost every piece of it, if you like the comparison.
When you outsource the build to a [huge] factory and make use of extensive CNC and machinery in general, for me it's not worth the price they're asking for. There's not too much love in putting some wood in a machine and press the start button. I hope you get my point.
The decision is up to the OP