Huuu well... Kinda depends on how you define "cosmetic perfection".
If it's about fancy shmancy flamed maple tops, uber-arty inlays, gold plated hardware and the like, then I couldn't care less. Err, wait - I do care, in fact : I just don't want anything like this on my guitars. I want a f... music instrument - you know, something I'm gonna play music with -, not a piece of overdecorated woodwork to hang on my wall. If that matters, two of my fav' guitars ever are the Telecaster and the Les Paul Jr - very raw stuff, yes.
Now if it's about build quality, then it's something else, and I'd be less confident in the overall build quality of a guitar where dots or pots don't line up evenly. I don't mean this would make the guitar sound bad by itself, but given that lutherie is about 1/10 mm precision, I wouldn't trust a "luthier" that's not even able to do a proper job on such things.