OK my update. Owner 17, annoying 2019 4Runner rattle/creak/thump 0.
Did 2 things. First, I jammed in some Amazon acoustic foam like suggested. But I also replaced the grab handle above the door. It had a tiny bit of play where the driver side door grab handle didn't, and when I removed it, I found one of the little prongs was broken (the thing the screwdriver is pointing at) ... I guess it was broken when installed:
I don't know if that was enough that it was moving around when the car flexed or what, but the noise is gone. Not sure which did it as I did at the same time.
Part number for whoever needs this later.