Push in on the trim if you're drilling new holes into the fiberglass. If there's an existing, but useless, pop-rivet, leave it in and add a new one. Don't drill through the bottom edge of the trim, as you'll make sharp edges to find with your knee or your fingers! (You're drilling through the top of just one side of the trim).
When you use the wrong length pop-rivets, there are some other sharp edges to worry about!