There is typically 4 ways to make jewelry
There is lost wax casting-where the design is done in wax and then cast in metal, there is metalsmithing-where the work is done with metal, there is wirewrapping, and then there is snap settings-premade settings, usually cast, that all you have to do is add a standard cut stone to. For obvious reasons custom cut cabochons are not usually used in the latter type. For the other 3 types, the jeweler may have a design in mind and then go looking for a cabochon, or find a cabochon that "speaks" to them and design around it. Jewelers can go through 1000's of cabochons looking for just the right one. And it can be very frustrating when the one they find is out of their budget.
Why are custom cut cabochons so much more expensive than standard commercial ones?
The main problem of course is the product we sell. We sell a product that takes millions of years to produce, is sometimes found only in one area, and many times the deposits get played out. The natural stone materials can even change in pattern or color from one foot to the next of the deposit! Often you don't really know what you're getting when you buy the rough, until you actually start cutting it. It is not like you can just pick up the phone and order 1000 more hamburgers. And there is no cost control.