It's really not that hard to keep your books straight if you're a small home FFL. Gun in date and description (SN, cal, etc), , who it came from, date it left, who it went to. In Colorado we have an online background check, so I don't have to phone anything in. It gives us an approximate wait time, so I know how long I have to entertain my guest.
But being a home FFL without much, if any inventory for a customer to play with at any time, I just have to entertain the customer with my incredible wit and charm (or if it's dove season, we'll go walk the ditch line). It's just 10-20 minutes of potential awkwardness.
But I can also understand why bigger dealers would charge more. And in some states the dealer is charged for the background check (CA for example).