Wow! If it's permissible to go up the MR and down the MT without a permit, that's news to me. My partner and I have done just that multiple times, and we were checked for a permit on the way down each time.
My understanding has always been that, while you don't need a permit for the MR (provided you aren't staying overnight, in which case you need a wilderness permit), everything on the Main Trail between Lone Pine Lake and the summit is considered the "Whitney Zone", and use of this section requires a permit - regardless of your point of entry or the direction you're traveling.
If the purpose of requiring permits in the first place is to regulate (and limit) use of the Main Trail, allowing people to ascend the MR and descend the MT without a permit doesn't make any sense.
I'd love to see some other people weight in on this issue. Perhaps I've been wrong all along...
(It's happened before)