My understanding is that the permits I obtain allow me to ENTER the wilderness once. They donít 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 donít go all the way to the trailhead, they could require a new permit.
I agree you shouldn't be able to go in and out of the wilderness repeatedly over a long period (especially multiple times from the same trailhead) and have no problem with the exiting and entering different trailheads being forbidden, but allowing you to leave the wilderness for a night to resupply is what the rules have been until now (for through PCT/JMT hikers).
This seems to only cover Inyo Forest trailheads, but that's a large chunk of the PCT/JMT.
And I'm about to put my first JMT lottery application in tomorrow, so the timing is particularly annoying.
Ironically, if I can't go southbound, Northbound permits might be easier to get at Onion Valley (Whitney exit has always been the biggest challenge).
Added: I just looked at some maps and Mammoth might be outside Inyo so should be safe. In fact it looks like the JMT technically leaves the wilderness briefly at that point.
Onion Valley is the biggest challenge if they actually enforce this somehow.