The Pine Creek Trail in PA passes through, I believe, two PA forest jurisdictions. There are "public" campgrounds in both. Just like in your case, you need to contact both jurisdictions for permits if you plan to stay in both. Seems like a bit of a PITA, but it's the nature of the beast. Don't know what a night costs. Possibly free. $40 for a primitive site is nuts. A U.S. Forest Service camping area like that would be free.
As for the idea of reservations/permits, the responsible authority wants to know who is going to be where when.