A theory:
I think properly custom build/hand built guitars have a lot of idiosyncrasies
Partly these could be seen as faults or quirks but lend a degree of character to an instrument
I was lucky enough to play Brian May's handbuilt red special guitar and it was a dream come true
But that guitar felt horrible to me, but had a uniqueness that was unmistakeable and I'm sure Brian feels that uniqueness too and wouldn't wish to play anything else
I have played a lot of great CNC made guitars that once well set up absolutely slay
Really well designed, and crafted (by machine - but who cares if it's that good)
But you could replace that guitar with any other that came off that production line and they too would perform equally well once set-up.
The trouble might be that as mega fantastic as those guitars are - they are replaceable and you might not notice the difference whereas if you got used to a handbuilt one, and tried another guitar it wouldn't feel the same - you might long for the original guitar
