I think it boils down to quality control/construction.
The maple you can find in a squier, can be the same quality as you find in a ken smith, if you put a Fodera pickup and pre on another bass with the same woods, it will sound the same.
i know boutique means that you pay more for a better fretboard finish, neck joint, hardware, aesthetic etc etc but..
I've tried many boutique basses with single coil configuration, and the end result is almost the same: a Marcus miller/pastorious, fender jazz bass tone, in some cases a good pre can give you more power and tonal options.
You can see very repetitive between luthiers from around the world, all converging on the same, Hipshot tuners, obp3 aguilar pre, Bartolini pickups, (hey i'm not saying this is bad) different basses using the same parts will sound the same at the end!
Concerning basses, and basses alone (not the amps, the player or whatever else have you) I disagree. I've played plenty of Squiers, plenty of Fender and a lot of production basses in general. Some were great, some not so much but I think that to assume that you get the same quality components in a Flea Bass or Squier that you get on a Nordy or Fodera is just silly. The cheaper one my sound better to you (a matter of preference), I know that's happened to me before, but I can say with near certainty that the overall quality of the instrument would not nearly be on the same level.
I understand that even after a certain point in quality (price?) the point become moot but that doesn't mean that the components that went into the bass are any less significant.
Beyond that, yes, many bass makers use similar parts but they all sound very different. Brubakers use the same electronics setup as Elricks and sound TOTALLY different and the same goes for a lot of other companies too. Until ou've actually done an electronics swap like you say, I don't think you can say whether or not it will sound the same. It may or may not, but I don't think you could confirm that without trying it.
