What the hell, I'll elaborate.
There's a misconception that many woods used on boutique instruments are rare and/or costly. As far as endangered species, that doesn't cover the majority of basses. What non-fancy endangered woods are you referring to?
I mentioned fancier woods because I've seen that mindset when referring to boutique builds. Typically by folks who haven't priced woods. The more figure, the higher the price... but what is that price? It's less than most might think. Take Spalted Maple. It's not rare, it can be difficult to work with and it used to get thrown away before figured woods became popular. In that respect it's like raw chicken wings. Used to be among the cheapest part of the chicken, now it's more than legs and thighs. Demand.
I'm stating that what drives the cost up on higher end instruments isn't usually the materials... it's the craftsmanship and everything that goes with that. It is not the items you said that drastically push the price up. Many tend to think that wood, hardware and electronics are the big expenses. Experience and the cost of doing business are the big expenses IME.
Gold hardware typically might cost a few dollars more than chrome or black. A $300 top on a $5,000 bass didn't really push the price up drastically. And so on.