I have a friend who makes exotic, high-end custom acoustic instruments- a heavily optioned harp guitar with enough inlays on it can top $20K.
Though hanging out with him, I've been surprised to learn how many heavy hitters in the boutique scene are working part-time, sleep in their shop, or have some other means of support.
If you're an individual creating instruments at the Dingwall/Fodera/FBass/Roscoe level and can't afford much in the way of automated tooling, $3,500 per instrument is a hard price point to hit. Building at that level of perfection is extremely time-consuming. You can contract some of the nasty stuff like finishing out to other specialists, but they aren't giving their services away either.
Getting into CAD is a bear, too. It isn't just about having enough money for the machines. You have to either hire creative professionals who can do the programming, or learn how to do it yourself. Either way, the design and development phase is hugely time-consuming. Paul Reid Smith, Jean Larrivee and Sheldon have managed the transition, but a lot of other ships have sunk on that particular reef.
Gibson isn't really representative of many other guitar brands. Like Martin, they're in a weird branding situation. It almost seems like the more unreasonable their pricing is, the more desirable the product becomes.