If we're really talking about
cost and not
worth or
value, then this thread has probably already hit on a lot of (all?) the costs.
Posters have listed the tangible stuff like the wood, parts, etc., as well as tools/machinery and the cost of their upkeep and parts. There is some variation based on "real" or "perceived" quality of different components as well as their scarcity.
Posters have listed related business and life costs that contribute to things like overhead -- renting or buying a workshop/buildspace, insurance, marketing, IT, accounting services, etc.
Posters have pointed to how there will be variation based on cost of living/cost of doing business differences linked to geography. Vinnie and Joey, or Roger, for example, do their thing in NYC. Not cheap.
And posters have pointed to labor costs. There are some macro aspects to it, like factory worker vs individual builder/craftsman and how that affects cost. It's also interesting to consider that "hourly labor" costs might vary by individual builder, and why that might happen. Once we remove something like cost of living/cost of doing business variation, I guess it's probably similar to other businesses where hourly labor costs might vary -- experience, reputation, etc. Two lawyers may be similarly capable of drawing up a will for me, but may charge different hourly rates (assuming for the moment that the rate excludes costs outside of the time each lawyer actually spends working on my will). Ideally the one who charges the higher rate has greater experience or expertise, and catches small things that the less expensive lawyer might not -- asks me particular questions about assets that I would want distributed upon my death that the less expensive lawyer might not have been exposed to yet in estate work, for example. But, if my estate planning needs are fairly straightforward or are somehow less important to me than they might be to others, then the cheaper lawyer might be just fine for me. Or if I had extra resources I might be willing to spend a bit more on what I would hope would be more thorough and thoughtful writing of a will. I guess this is one of the places where the dance between cost and worth/value happens, with the latter interacting with my wants, my needs, and my resources.
With a smaller shop or "boutique" or custom bass, part of what my interest might be in paying more for it may have to do with my perception that a particular builder or business will pay some extra attention to my instrument and maybe catch some things or be attuned to things that a lower cost alternative might not.
Maybe some of the labor costs aren't that different from what happens within the organization for which I work. There is an "unloaded" rate for my time and a "loaded" rate for my time. The "loaded" rate accounts for stuff like overhead and costs to the organization, and things that are typically outside of my control (e.g., change in the rent the organization pays to the building owner). The "unloaded" rate is representative more directly about what the organization considers my value. Based at least partially on an assumption that my greater experience in my job, and the increased variety of the work that I've done, my "unloaded" rate has risen over time -- I supposedly bring greater value to a project. (Ha! The wool is over who's eyes...?!)

So, some builders may cost more over time for similar reasons, and we will each vary in the extent to which we perceive and value their experience and expertise.
And maybe one day I will want to buy a Rick Kelly bass because I know that he really does build each one by hand and he seems like a nice man and he's a fellow New Yorker and I like Carmine St Guitars, and then the price becomes less relevant in relation to the "actual" cost for me because I am valuing other aspects of the transaction beyond the instrument itself. That said, I'm still not going to buy one if I haven't played something he's made and liked it! (Just an example here prompted by an interesting article about Rick and his colleagues and his shop in this past weekend's newspaper.)
...jeez...shut me up...what a crazy post this is!