If it was my boat, I would remove them, and just use smaller stainless bolts and captive(with the plastic insert)nuts with washers to fill the holes.
I have relocated, and removed hardware on various boats, and that is what I do rather than screwing around with patching the hole and then matching the finish.
YakCatcher Rod Holder
Kayak Deck Gear Bags
Bent Shaft Canoe Paddles
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