My experience with getting a pass for Trail Pass/Cottonwood Pass area was that even though I followed all the instructions, I had to call to actually get my pass mailed to me.
At first I tried to get a pass from a different agency on the Western side of the Sierra (for the High Sierra Trail) by emailing a PDF form but that never worked. I tried twice and was always rejected and the rejection always went to my spam folder which was really annoying.
So I moved over to trying to get one from the Eastern side. I think I tried via the USFS website with no luck. Then someone said to use recreation.gov.
I was able to get my pass through https://www.recreation.gov/permits/233262. At first when I went there, there was no availability for the entry points that I wanted, but then one Monday afternoon a bunch of new permits were released and I was able to fill out their form, set my itinerary and pay for my permit all in one go. They included instructions on how to request an email copy of my permit and they said that walking in to pick it up was not available. You have to request an email copy. So I followed the instructions for that.
I heard nothing from them so I requested the email copy again a few days later. Still nothing.
So the Sunday morning 8AM before I left, running out of time, I called them on the phone and miraculously someone answered the phone. That person was very nice and emailed the permit to me right after we hung up.
Those were the steps I had to go to get this done.
When I was on the actual trip, I saw two rangers. One of them asked to see my permit only because I reported to her that I lost my hiking friend a few days prior. She was very apologetic about asking to see my permit. She did want to see the itinerary only so she could call other rangers to see if they’d seen my friend near any of those places. I had actually sort of followed my itinerary, but I told her I didn’t actually camp at all those places. She said yeah, the whole itinerary thing is pretty annoying and nobody expects you to stick to it.
The second ranger didn’t ask to see permits. He was very friendly. They all seemed very friendly. They just wanted to be helpful and do something other than just collecting trash. SEKI is pretty trashed right now. I was disappointed.