Just took my truck (2016 Sierra SLT Crew) into the dealer for a 5,000 mile service.
Since new I have experienced moderate/severe clunking in the 1-2 upshift and 2-1 downshift. Being a long-time reader here of people's experiences, I decided to let it hit the magic 5,000 mile number before going in to address the issues. At about 4,800 miles, things really calmed down and I would only notice the shift clunking every once in awhile. Saturday when I took it in for service (at around 5,100 miles) and mentioned the trouble I'd been having, the dealer said there was a software update for this very issue, and that they'd re-flash it and then do the fast learn. WOW! Now it drives like I expected from day 1. Beautiful! If your dealer hasn't run this latest update for you yet, get them to do it! I couldn't be happier!
I did also tighten the leaf spring bolts a few months ago, which did make some difference, but definitely the transmission was part of the clunking as well. I too agree that sometimes I hear the fuel sloshing around in the tank (which I've never heard on any other vehicle), but it's not the same sound as these transmission/rear-end clunk noises.