I have a gen 1, so keep in mind that a lot has changed but a lot of the concepts haven’t.
When I had the stock shocks, I felt something that sounds a lot like the same thing you are describing. Felt like something was loose. I would feel this over wash board type chop, mostly offroad, and I would feel it in the floorboard. Once I switched to aftermarket shocks I never felt it again.
My truck was bottom perch with geiser coils and mid perch with stock coils. Felt it with both setups. I never checked the nitrogen in the stockers and that may have been an issue. I more or less assumed it had to either be the rubber bushings or the way the internal bypass worked.