You did miss a couple of expenses FFL's have.
1 Liability and theft insurance (I'm sure in not the only person with coverage)
2. Credit Card Monthly account Fee's (just to have the account)
3. Phone lines
4. Initial expense for starting up , Construction, App Fee's etc etc
5. Misc expenses (ie accounting)
6. Time, When i do a transfer for a new gun owner they always ask questions about the firearm they purchased elsewhere, A 15 minute transfer can easily become a 1 hour transfer and Q&A session. Im more then happy to do it but it does come at a cost to us in time. You will have to look hard to find a customer i rushed out the door due to questions.
So that 25 transfer fee is in no way profit
I'm not justifying those FFL's that charge higher then normal rates but i am justifying the 40.00 including NICS that most of us charge.