There are a LOT of reasons. Some is that small makers don't have the economy of scale that big makers get. Fender probably uses more 250K pots in a month than Dan Lakin uses in a year. Then you add in the wider range of instruments that a mass-market company like FMIC makes- that allows them to spread the fixed components of cost around a lot more.
Laklands (I'm using them because I'm really familiar with them, BTW- I've never played a Sadowsky and only a few Ken Smiths and a handful of Pedullas, and none of the other "high end" or "boutique" instruments) have impeccable finish, fret work, nuts, etc. Just the nut- almost NO mass-market instrument I've played in over 30 years has the nut cut correctly. They're all too high. Why? COST! To cut a nut correctly one needs to spend a lot of time, and it's pretty much a trial-and-error process. Loosen the string, cut the nut to where you think it should be, retune and test, repeat as needed. If you go one pass of the file too far, you have to start all over. So, it's cheaper to leave it a little high. That's what FMIC, Ibanez, Schecter, Peavey, Gibson, et. al. do. The boutique guys take the time to do it right.
Same thing for fret work, soldering etc. There was a thread here earlier this week about the rubbing compound Fender leaves in the control cavaties on their instruments. That stuff is abrasive and often corrosive. It wrecks pots and solder joints. But it takes time to remove it well and it's hidden so FMIC (among others) leaves it in there. Lakland doesn't. And how well shielded is that $900 mass-market Jazz bass clone compared to a Joe Osborne?
Most boutique guys also spend a lot of time making things LOOK great. Lakland inspects the body blanks and determines what finish will look best on each body. FMIC et. al. just spray them as they come down the line- no matter what the grain is, if it's sunburst day, they're all sprayed 'bursts.
The other factor is that after a certain point, each increment of "quality" costs more to build than before. Going from say $500 to $1000 is one jump. But to get that same level of jump beyond $1K, it might take another $1000 instead of the $500. That's because it becomes more labor intensive so you loose the advantages of mass production.
Lots of things to consider here- and I have stuff ranging in price from my MIJ Sting to my US Lakland Deluxe 494. They're equally "good" for my needs, but the things that make them work for me cost more on the one than the other.
jte