But again, over the gunwale is not good.
Over the bow rail would be high enough - but that's really bad because it severely restricts your vision.
The aft gunwale, keeping them high enough, would be fine. Maybe those rod holder racks is what you're looking for?
A couple pieces of dense foam (even pool noodle) and a ratchet strap would work on the hardtop. Or you can go crazy and get something premade - lot's of options - easy to find with searching. Look for what suits you best.