I also followed that thread and tried that fix but it didn't work for me either. My sunroof had three distinct rattles. I pulled the headliner last week to see if there was anything I could do about them. I found a couple loose nuts holding the rails right above the rear doors. I found this odd because there has never been any work done on the sunroof. Next, was the linkages that hold the glass itself. They are loose but I don't really see a way to tighten them. If I cycle the sunroof, the glass and linkages stay tight for about 5 minutes then start rattling again. Since I never use the sunroof anyway, I shoved a rubber shock bushing in each rear corner of the sunroof between the glass and the frame. Last, I found that the sunshade fits very loose in the tracks and was also slapping the thin metal crossmember that is between the shade and headliner. I pinched down the sunshade tracks slightly with some pliers and shoved a piece of foam between the sunshade and crossmember.
I know these are not really fixes but they do solve the rattles that were driving me so crazy I almost traded it in a couple weeks ago. Like I said earlier, I never use the sunroof. Maybe my wife does but I never do. I wish both my 4runners didn't have them. Also, I'm screwed if anyone tries to open it like this so I was sure to tell my wife and kids to never try to use it. Quiet as a library for now........