Even New Jersey (with the exception of the NY/NJ Port Authority Police) recognize the FOPA. In fact, with one important editorial change, the exact language of the FOPA is in NJ statute and can be accessed from the NJ State Police web site. The critical difference is that the FOPA says if the vehicle has no separate trunk, the firearm OR ammunition must be in a locked container. The NJ version says the firearm AND the ammunition must be in a locked container.
There is also a legal opinion on the Pennsylvania Firearms Owners Association web site that argues the FOPA doesn't apply when traveling to or through a neighboring state (such as PA and NJ). I don't happen to agree with that view, because to get there one would have to argue that traveling from one state to another is somehow NOT interstate travel, but the argument is that because the FOPA requires that possession (AND carry) must be legal in the state where you start and in the state where you end, then the FOPA covers only intervening states. Too deep for me.
But the FOPA does require that the firearm be unloaded, and either in a compartment separate from the passenger compartment or in a locked container. So in the incident being discussed, the FOPA could not apply since the mode of transport did not comply with the requirements of the law.
So he's very lucky that ALL he lost was a pistol and some dollars. He could easily have become a convicted felon and lost his RKBA for ever.