Total cost is a combination of wood cost, likelihood and quantity of waste, possibility and cost of a ruined piece that needs to be redone, amount of labor to execute (different woods have different work/glue properties), and who knows what else. That said, I hold the unpopular belief that some of the pricing structures Alembic uses aren't particularly fair on the surface.
For example, the quote generator will tell you it is $800 to add tulipwood in place of a flame maple top, or $1000 for cocobolo. Why, then, would it be $800 to replace a piece of cocobolo on a Signature Deluxe bass with tulipwood? I suspect that some of these things are just the simplistic implementation of the quote generator, but I have never tried to place such an order with Alembic to know how it would actually be treated.
Then there's always the srtaight capitalism answer. The price is impacted by demand, so popular options can provide better profit margins. In any case, and while I disagree with several aspects of the pricing model, I respect the right of Alembic to set pricing as they see fit. Many people must think it's a fair deal since they continue to churn out basses with a several month waiting list.
As a side note, do you have any idea what it costs a fast food restaurant to serve you that 20oz soda for which they charge you $1.39? 20 years ago the answer was $.04, so it could be as much as $.15 these days. You want to complain about a profit margin, take a look at that one...