A fundamental prerequisite of the FOPA is that possession (or "carry") of the firearm must be legal in the place where the journey begins and the place where the journey ends
I am assuming that Meckler's journey did begin in a state where possession is legal. Meckler is a CA resident, so that is a logical starting point for the journey. But so far there is nothing definitive on that.
Constructive possession under New York law could indeed be problematic with regard to FOPA. If he's smart, Meckler left the gun in a locker at the airport during his little travel break.
If the State of New York is smart, it will drop the charges.
Alan Gura must be teething at the bit on this one.
If he isn't involved already.
There's a good possibility this case has been tailored on in advance.