I’m a peakbagger, not a through-hiker, so I don’t know anything about special rules for PCT/JMT hikers. My understanding is that the permits I obtain allow me to ENTER the wilderness once. They don’t allow me to spend the whole summer entering and exiting the wilderness at will. If I exit the wilderness for a resupply, even if I don’t go all the way to the trailhead, they could require a new permit. Of course, if a SEKI ranger checked my permit at Kearsarge Pass after I got a shower and some supplies in Independence, they would be hard-pressed to establish whether I had ever exited the wilderness.

There are many ways to manage wilderness permits. A trailhead quota with ONE unlimited stay in the wilderness is one solution, and it’s not a bad one. Some people will stay one night and others will stay over a week, but congestion at campsites near the trailheads will be manageable. If some hikers exit and reenter the wilderness, the congestion at those campsites will increase. At that point, the USFS/NPS can ignore the overuse, restrict exiting and reentering the wilderness, or lower the trailhead quotas. Which do you prefer?