I've been going over the rivets... is that the wrong way??
Unless you're using cast wrap, most media won't fully conform to the higher profile rivets or screws in this case. Depending on the competition in one's area, the local pricing and longevity expectations can dictate whether or not one uses cast or calendared media.
When we remove the screws, we always dab the holes with 94 Primer with the tip of a swab in case the manufacturer laid down a bead of silicone under the panel seams. We also use a drill with a clutch and not an impact driver to put the screws back in so we can adjust the torque to the perfect amount to not twist the media.