Yes the edges could scratch the gel-coat if you just roughed them out with a saw or plasma and then hit the high spots with a grinder. On the other hand; if you laid the assembly on a belt sander that had a fairly fine grit belt and ground the surface that touches the hood so it was both flat and smooth, then carefully chamfered the edges of that with the same belt, to remove the knife edges, then took the mating surfaces to a cotton buffing wheel that was impregnated with jewelers rouge and polished them, then you would parobably end up with edges that wouldn't scratch nor would there be a necessity for a rubber pad that could discolor the pretty yellow gel-coat.

Let's remember that this is the "Precision" forum after all. Hammers, chisels, and rough cutting devices don't fit here. It's also probably not polite to talk about how a man could possibly drill through the plastic engine air intake horn that sits up against the hood undersides, if he wasn't careful when he drilled the hole in the hood