I think a parts bass and a custom bass are two different things, although they have some overlap.
With a parts bass add the cost of all the components, and that tells you how much someone is charging to assemble it.
With a custom bass you have to factor lots more in- design, planning, artistic merit, sourcing rare or exotic wood, dealing back and forth with the client on his exact specs, expectations, and dreams. Allowing for possible revisions, and further custom work. Often parts basses are built by someone with very limited workshop space and speciallized equipment, which costs money.