Glenn's aluminum rivet idea is a good idea, but you're going to end up with rivet heads where you used to have smooth seat.
This is going to devolve into a pissing match here, but from your post- 'rivets...intriguing', my assumption is that you don't have very much hands on experience with redneck rigging. (called it something else where I'm from).
Glenn could likely fix you up with his gun and his rivets. If you just go out thinking to buy a rivet gun and whatever rivets fit that gun, with no background in failure, well, you're likely to end up with bigger holes in your boat and more yelping from the dog.
Rethinking this, I think all you need is a pocketknife. Or a kitchen paring knife.
Whittle a little dried twig to a point, just enough to wedge down in the holes. Lightly slather it in semi-set up JB Weld regular mix and then hammer it down with a punch (a small brad head will work) until it's just slightly below the surface. The epoxy will form a head over the hole. It is much more viscous than you would think. Wipe off the excess and let whatever is left flow into each hole.
Wipe off the excess JB from the surrounding area (it will top itself off), let it set, sand the JB and surrounding area down to bare aluminum, primer with self etching aluminum primer and then paint/camo over it. Do it right, (easy) and you'll never know the holes were there.
I've made a ton of mistakes in nearly every area of my life and I'm not good at admitting defeat, but beautiful boats and her temperaments have flat beat me down. I now wholly submit myself to dudes who have been there before. Call her a slut, I don't care...just help me fix this bitch. It is just that until it's ok again. Argue?
That's how I feel anyway. Spend enough time messing around in boats and you might feel the same. Sorry for the pup's toenail. Another use for the superglue/baking soda trick.
You could just do that.
Best of luck whatever you do.