Tom, I certainly did not claim that all of the wilderness rules and permit regs made sense. I just found what I found on the various web sites. Also, I have found a little bit of inconsistency within one jurisdiction, but I think that is more a matter of one web page being updated and a second page is not yet.
Now, what I was referring to was a start from the west side of Sequoia National Park, e.g. Giant Forest, and coming east to Whitney. What I was originally thinking of was Giant Forest to Whitney on the High Sierra Trail, and then a complete reverse course back to Giant Forest. For that, it is a standard Sequoia wilderness permit, and the only trick is that the permit issuer must note that it includes the Whitney summit or Whitney Trail exit or whatever.
This gets a little messy for Shepherd Pass. Here, you are starting within Inyo N.F., then crossing into Sequoia N.P., and then exiting back out through Inyo N.F. I don't know this for a fact, but I am guessing that this goes into Inyo permits and quotas and has very little to do with Sequoia permits and quotas, even though it obviously crosses Sequoia land.
For what it's worth, in 1976, I was slowly approaching the Whitney summit, and a Sequoia park ranger was descending hurriedly at 3 p.m. He stopped me to check my permit and then we continued our ways. That is the only time in all of these years that I've seen a Sequoia ranger anywhere around there. National Forest wilderness rangers tend to be all over on the east side, because that is where the most people are.
Don't expect this to make perfect sense. After all, these are agencies of the federal government. Besides, the Forest Service is within the Department of Agriculture (multiple uses) and the Park Service is within the Department of the Interior (protect only). These are your federal tax dollars at work. Also, they change their rules and policies periodically. I'm guessing that the two agencies are not good about sharing any kind of quota use.
I submitted my Whitney Trail dayhike permit reservation request for the lottery, and I submitted it for one more hiker than what I know I have. We will see how that turns out.