Normally there is a small piece of plastic type material that is attached to that spot where the hatch 'foot' sits.. at least on the three that I have had... I actually put a thicker piece of rubber ESD mat in that location on my Aero to cushion it...

Looks like your going to need a little paint touch up and then cover with a piece of thick mylar or some other material to prevent the vibration of the hatch from rubbing..

The other thing is to find out why your hatch is vibrating so much... sound like it isnt tight... you can adjust the little 'feet' down to get a snugger fit.....