What is your point?
I said they are not gonna call the cops, they dont routinely do that at Logan like they do at JFK/LGA/EWR. Therefore, why would it matter what the OP's license situation is? He IS within the bounds of FOPA and beyond that, history tells us that he is extremely unlikely to encounter a cop who would jam him up and make him tell the judge all about FOPA.
People are overthinking this as usual, of all the airports Ive flown out of with firearms, Logan is one of the few that I can say that I have never even had somebody so much as look sideways at me. At almost every other airport I frequent, Ive had at least one idiot ask stupid questions, call higher up's, try to tell me something was illegal when it was not, etc. This has been in much more gun friendly states than here.
Another relatively easy situation made complicated.
Take the damn bag and hightail it the hell off airport property. Nothing on your bag screams "firearm" and nobody at your destination will be the wiser. Rent car, drive home, don't get pulled over, crisis averted. Yes you are still doing something illegal but your chances of getting in trouble go from damn near 100% if you go to check in the bag again to about .0000000000000000000000001 if you are smart about driving out of enemy territory.
Thats what I would do. Worst case scenario, my trip is delayed, I miss a flight and might eat a few hundred bucks if I cant get a refund from the airline. Beats jail.
*Assumes handgun(s) in normal looking bag. I have no idea on long guns/cases that scream "rifle" (could it not be skis, hockey sticks, etc?) or what the deal is with NY/NJ port authority on long gun regs if treated any different than handguns.