I had the exact same issue on my Model 3, looking at the bolt on the left compared to the right side, the right side bolt was tightened down a couple of turns more than the left. I tightened the left bolt to the same height as the bolt on the right side as the left bolt had a wear spot that was hitting the edge of the upper trunk hinge (causing the random clicking noise of rough roads). I then took my car for a drive down the same road that would always produce the sound and the clicking noise was gone! Thank God as it was driving me crazy. Looking at the hinge, I can not for the life of see what purpose it serves? But regardless, I’m glad the issue is resolved and the fact that I didn’t waste time taking the car to the local Service Center.
I think the screw is to align the trunk panel to the rest of the car. If you screw it down, you might notice that your trunk lid sags a bit compared to the adjacent panels. But glad you were able to silence the tapping!