I don't know why you could not use pop rivets on the camlocs. The aileron brackets are pop-riveted on, as are the lift strut attachments - all structural. The rivets are there to hold the camloc in place. It will not pull through the fiberglass. Just make sure they are long enough to set properly.
I believe the new Kitfox cowl fasteners are Skybolt Cloc 2500 series. Go to their website (skybolt.com) and download the engineering catalog. The catalog describes proper mounting and other selection criteria.
The upper cowl edge thickness is definitely not consistent which can cause a wavy look and high or low spots. I'm trying to figure out how to best resolve this...