That's the definition of a toss-up: it is technically not within the law, but they choose to not prosecute it.
Since the first GFSZA was overturned, it was (barely) modified and re-enacted. You're right that it's never prosecuted in clean cases, but I have seen instances where it was added on as plea bait in serious felony drug cases. It's also used to determine sentencing points, which don't even require a conviction on that particular charge, just a finding of "conduct of the crime".
Sorry that I can't cite any particular cases. I retired in 2014 after dealing with more case files than I care to recall.
I have no doubt that it's been used in dozens of other cases for leverage, etc. Particularly drug cases where they caught some guy on school grounds (or within the GFSZ radius) with drugs and a gun, etc.
It's just that I doubt (and would even wager money on) it never being used in the context that we're talking about here. Mainly because I don't think USA/AUSAs are that dumb to know that its something that would blow up directly in their face. No jury is going to suck for something that is that illogical. It's plainly obvious what the real intent of that part of the law was, too, and if the permit satisfies that intent, then there is no "crime".
This isn't the only federal gun law that's broken like this. I've never heard of that law that says an "FFL must obey the laws of the state of residence on long guns" garbage to be enforced, either, at least not at the level of a real court case. BATFE probably uses it as a wedge administratively to force compliance though... but they don't really want that particular garbage scow to go very far in federal court, because the way that law is constructed it likely is either unconstitutional or it violates other commonly accepted tenets of law in the US.
Same thing with USC 922R, although I think in that case most gun owners misinterpret that one- a strict reading of 922R makes it painfully obvious the law is really only directed at importers or manufacturers (and as far as I know, it's only ever been enforced that way) yet every other gun owner shits their pants over it for no good reason.
Thus, this whole "Well, its invalid because NH could possibly maybe issue a PRL by the hand of someone who isn't a cop, but actually never does that" stuff, is in the realm of "If it weren't for my horse, I wouldn't have spent that year in college...."
-Mike