I didn’t put anything between the flanges due to the tight tolerance there. I’m sure your car is the same, but, you probably saw how the flanges rub against each other just from shifting the roof up and down with the bolts loosened. I guess it’s possible since that is a metal on metal area there could be noise generated from those rubbing against each other, but, that wasn’t an issue for me.
The tape should be thick enough. It’s really about getting a different material between the 2 metal surfaces so they don’t interact. That’s why the shelf liner Marc used works. You could probably layer another strip of the felt tape on the existing one if you wanted.
IMO, first, I think you need to adjust your bolts on each side so they line up with the factory marks. Let’s eliminate alignment so we can be sure that isn’t the new issue. I definitely remember when I did mine the sunroof shifted down almost an 1/8 of an inch or just under.