I think all the pax has to do is fill out a gun tag(?) and get a lock-box from the airlines, and he's legal if he has a permit and the gun is registered. I'm guessing that ammunition must not be in any proximity to the gun.
We've had a couple of gun incidents involving pax and employees and stupid decisions. Now here's a bit of advice, don't ask TSA, because they seem as clueless as the inquisitor! This was my own observation, though.
I'm guessing this guy was a rookie. A bit of advice that I read on the web is that if the gun owner wants to inquire about his firearm, he must never start the sentence with "I have a gun...!"