This is the exact opposite of overpriced. You have a single dude who isn't getting bulk discounts on parts and doesn't have a staff doing professional quality woodworking followed by hand-wiring electronics often with variations based on your specifications. Subtract overhead (space, tools, electricity), parts (including ones that don't pass QC and can't be used), and taxes and he probably isn't making a whole lot.
Add to that the fact that part of what you are buying is a direct relationship with your amp maker and $3k is a bargain.
I guarantee that the guys who do that are in a "labor of love" situation like most luthiers (or musicians). Sure a handfull of guys get rich but the overwhelming majority don't.