When the rules changed, we lost most of the kitchen table dealers, as the rest had to prove a place of business and operating hours. At least that is the continued point by the BATF in issuing licenses.
Further, the few kitchen table dealers don't even advertise. I've yet to see "$25 internet FFL transfers, call 1-myareacodeandnumber." At least that could give the appearance of trying to be in business, which the BATF is attempting to force. Hence the requirement to collect and report sales tax, hold local licenses, etc.
Add those annual fees to holding the FFL, to, it's not a cheap hobby.
As for the OP, he didn't get stuck for the $50 charge, he successfully negotiated with the clerk and got it reduced. Let's not assume said clerk was working entirely on his own recognizance. Again, it was a transaction conducted over weeks of time, and he answers to the owner. It's quite likely getting a gun shipped in without expecting it - just forgot or whatever - made the owner consider the situation. He very well may have instructed his up front guy to ask for $50 in the future, and when the OP showed up, he did. The clerk very well may have been doing his job as required. Some owners with "buddies" who constantly take advantage of the relationship figure out ways to communicate they aren't happy about how they get used, or abused.
We keep banging away at the poor clerk when the real situation was doing his bosses dirty work. Frankly, not every customer is worth all the hand holding and high maintenance they demand - and those of us who actually work retail can give you about 100 pages of our anecdotes justifying what the clerk may have been doing.
Otherwise, it's a he said she said situation, and whether or not the negative future business was intended, that well may be the result. Choose whatever side you like, but don't insist it has to be your way or the highway, as we have no clue or statement from the other side at all. There very well may be details being left off the table.
I still stand on what I said - after weeks of waiting for delivery, more could have been done to nail down the details and prevent it. A third party arranged this deal with only one perfunctory conversation on the part of the OP. Is that the way you would do it?