Thanks OP for posting this. I recently flew the outbound leg of this (RGN-BKK-NRT-JFK-SFO) and wanted to share my experience.
I was actually in BKK and just doing a turn at RGN, so I booked an earlier BKK-RGN flight on PG that gave me about a 4 hour layover in RGN until my RGN-BKK flight back, also on PG. I had hoped to get my boarding pass for the flight back in BKK, but they insisted that they could not check me in, and that I needed to visit the checkin desk in RGN, so it was a good thing I had arranged for a Myanmar visa.
When I arrived in RGN, I got through immigration and customs pretty quickly and headed to the checkin desk as my inbound plane was turning around and I wanted to see if I could change to the earlier flight back instead of hanging around in RGN for a few hours. The PG segment was booked in Y so theoretically it should have been possible, but at the desk, they saw it was ticketed by JL and said they couldn't make any changes to it, only JL could. I then asked if they could check me in and issue me the boarding pass for my original flight, but they said they could not, and I would have to wait a few hours until checkin opened for that flight, so I spent about 1.5 hours in the departures area just waiting for them to reopen checkin.
Because I was just doing a turn in RGN, I had actually booked a hotel for the previous and current night (I had an overnight layover), so that I could just travel with hand luggage. The checkin agents in RGN were able to issue me boarding passes through to JFK (but not SFO strangely). The next morning, I decided I wanted to try and use the express channel for security/immigration, so I headed to the checkin desk. That was my mistake. Since BKK was only ticketed as a "connection", they required me to pay a 700 baht airport tax in order to checkin again. I ended up having to pay that, and essentially that was the cost of my (non-essential) express channel. Oops.
Moral of the story is if you have one of these fares and have an overnight connection where you leave the airside, don't checkin at the desk again, or you may be required to pay the airport departure taxes!