I think it'd work either way. Let's say you wanted to buy a rifle from a custom shop. If an FFL in your town is a dealer for said shop, then you could buy one from him if he has what you want on the shelf or he can order you up one the way you want it. Or if you're buying direct from the custom shop, I'd guess you tell them what you want, send 'em a check and a copy of the FFL they can ship your new toy to, your FFL charges you a transfer fee of their choosing, the shop sends your rifle to that dealer, you pay your transfer fee, and everyone goes home happy.