Labor costs are the largest factor in a boutique, and one that people often neglect. The reality is that the parts are only so expensive (there are quality differences unless the builder is using stock parts from Hipshot, AllParts, etc), and wood is wood unless you're talking rare/beautiful pieces. Beyond that it mostly is how many people are required to get an instrument from start to shipped, and how much do those people cost. Frankly many small luthiers don't make very much money if you calculate an effective "hourly" pay. Plus they often either don't have health/retirement benefits (or short change those). Fodera gets called out all the time on TB as being "stupid expensive," and their prices have gone up over the past 5 years. But part of that is because employees have benefits that many take for granted, and they are in an expensive part of the country. So it is all relative. From the end customer standpoint the purchase price is an objective number, and if you can get your dream instrument for less money, then it is win/win. I'm sure some wish that Fodera was based in a cheaper part of the country, hoping that prices would be less. But it isn't. And part of what makes the place Fodera is that it is in NY, in the heart of a busy music scene where A-level players are common-place and often can be found at the shop. You don't get that kind of scene in many other parts of the country.
That isn't to say that Fodera is "the best" - they make a great instrument, have amazing customer service, and you pay a premium price for it. Whether it is worth it or not depends on what is important to you and what you're looking for. There are a lot of great small builders that also provide great customer service - and for less money. But it isn't a Fodera. Just like a Fodera isn't an Alembic, and and Alembic isn't a Ken Lawrence, etc. Tons of awesome instruments out there if you want to pay top dollar, and perhaps more germane to this thread, there are also really good production instruments that get you a lot of quality for a lot less money.