I've owned loads of custom builds, but they were all built for other people so I do understand what this topic is all about!
The two honest-to-God commissioned-by-me-to-my-own-specs custom builds that I have ordered are still with me and are HUGELY unlikely to be going anywhere else.
In truth, and in the interests of full disclosure, both basses have things that I could nit-pick about if I wanted, things the builder got 'wrong'. These issues (I can hardly bring myself to describe them as 'faults') are always going to happen unless you spend the entire build in the luthier's workshop, looming over his bench and preventing him from deciding anything for himself.°
In my (limited) experience the killer factor is whether or not you have a clear purpose for the instrument. Commissioning an instrument as a 50th birthday present to yourself, or because you like the luthier or something, is IMHO doomed to end in failure and disappointment. My two were both very specific orders to meet very specific needs.
º Other genders of luthier are available.