Hmm, Grizz? I'm not sure what you're saying.
If IS getting caught, if you get caught. You ARE indeed, in reality, breaking that state's law and you are, in fact, perfectly susceptible to arrest for that. It does happen and there are documented cases that have made the news and the rounds of the gun boards.
I don't grasp if you're suggesting that a lot of people breeze on through those states without attracting any officer's notice? Sure, of course they do! And it's wise to behave so, no matter how law-abiding you are.
Or maybe you're suggesting that there are many instances where people are pulled over, their cars searched, and guns found where the driver utters the magic words, "FOPA, FOPA, Alakazam!" and the officer chuckles wryly and bids them godspeed on their way because now the law doesn't apply to them?
(Remember, there's a great danger in considering that the legal situation is a certain way because of the cases you happen to know about, or DON'T know about. How many gun arrests are there where FOPA might apply, or you think it should apply, but those cases turn a different way and/or don't make a big splash on internet forums? Don't bet too much on it.)
It is important to remember that affirmative defenses like FOPA are "rebutable" -- meaning that sure, you said you were just passing through, but the DA isn't necessarily going to take that at face value. If he or she feels that they can prove you stopped off for the day to sight-see, or went out to dinner with friends, or whatever else that could turn that state into one of your journey's destinations, not simply a passing-through situation, then your FOPA protection evaporates. That's probably not going to hit the press as a "FOPA" case, because the FOPA claim was tossed out.
Now, sure, if an officer finds that you have a gun and decides not to apply his state's law to you -- which would be increasingly unlikely in these days where every officer's traffic stops are recorded on film and audio, thus lessening his/her willingness to turn a blind eye to a felony, on the record -- then that isn't going to make the papers, either. (Just like when an officer DOESN'T arrest someone he finds with drugs, or DOESN'T pull over a speeder.)
An officer in NY or NJ will be able to quote chapter and verse of what state law you're breaking. He or she may have heard of FOPA, perhaps ... call it 50/50 odds, but FOPA doesn't apply to them. It doesn't instruct an arresting officer how to proceed. It tells a judge how to instruct a jury, once you're prosecuted for breaking that state law.