STATE laws are the governing matter. What the ATF interprets as a pistol is whether it has no stock and if it was never originally assembled with a stock and barrel over 16". Other than that, they aren't too concerned.
But the STATE law going from one jurisdiction to the other is what a LEO will interpret. If that state doesn't allow weapons with barrels over a certain length, or states a maximum length for a pistol, that's the ticket. Literally.
There are also laws on transportation. If it's a pistol either state may, or more importantly, may not allow concealed carry loaded and close to hand. In this specific case if the weapon is a "firearm" or in a "firearm" configuration with VFG then it may fall under rules for transporting rifles - cased unloaded in the back. All that will be governed by the LEOs interpretation.
It also goes to why you even got stopped. Not getting stopped is what usually happens, states don't have border guards to inspect your vehicle or poke around in the trunk. Unless you are transiting NJ, then all bets are off. I say that because NJ has some really difficult out of state handgun prohibitions.
What a lot of the transportation laws originally tried to cover was poaching - and the resulting loaded firearms up in the front seat being used by poachers running the roads looking for game animals, usually out of season. Government likes to make rules and they use the rare circumstance to apply law to law abiders, so we wound up with no loaded guns in the vehicle readily available to stop one or two guys in the county jacklighting deer at night.
Now we have to deal with it. It's not the ATF, it's the local laws to consider.