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I'm in the middle of replacing my rubrail. Yesterday evening we took the rubrail out of its channel, drilled out the rivet heads, removed the channel, hammered the rivets in flush, and cleaned the gunwale.

This evening I drove the rivets into the foam with a punch, we slightly countersunk the holes, and filled them with West System Six 10.

Now for the two things:

The West System Six 10 is the way to go. It's pricey, but it works really well for filling holes. I've tried to put epoxy in a syringe before, and it's not all that easy.

So, when I drill the holes through the channel into the gunnel, should I shoot a little bit of marine caulk into each hole?

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I always use some ploy sulfide caulk on every fastener I put through the skin of my boat.

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During replacement of my rub rail on a 1984 Outrage I applied 3M4200 on each rivet shaft before inserting and after setting the pop rivet I used any excess and smeared in into the top of the pop rivet head hole.