It's funny this is my first post on here. I was on YT for years before this, but I couldn't find anyone with this issue. Anyways...
I've been having the same noise since installing my superflex coils ~5 months ago. I searched and searched but couldn't figure it out. I still haven't fix it yet, but I think I might have found a solution. In your video it looks like you are using the 5125 Bilsteins from Toytech. I have the same shock set up, but after hearing the noise, I searched on their site to see if I spec'd the shocks with the springs. I was thinking the shocks were bottoming out. Turns out, they suggest using the 5100 long travels:
"These are long travel rear Bilstein 5100 series shocks outfitted to work with your 3rd Gen 4Runner and
should only be used with our Toytec Superflex 024RCB coils or long rear lift coil springs. "
Bilstein 5100 Rear shocks for FJ/4Runner
After reading this thread, I don't think I'm bottoming out the shock, I think the coil aren't "extended" enough at ride height, so the coils are hitting each other during the suspension travel.
I have the 5100's in my garage to install this weekend. I'll chime in if it solves the problem...