Repair Small Holes In truck bed

[DLandes14]

Just looking for some advice here. I just bought my first truck, a 2015 GMC Sierra. The previous owner had a plastic tool box mounted behind the cab and they attached it by just driving in self tapping metal screws straight through the protective bed rail caps and through the metal bed rails. I doubt there was any sort of prep work done on the bare metal. I don't really plan on using the tool box so I removed it and the screws were really rusted and the very little bit of the holes I can see through the protective bed rail caps I can tell there is some surface rust to the inside edge of the holes themselves and possibly a little bit outside of the holes but I can't see much. I really don't care about the holes in the liner but I'm just concerned about what could eventually happen underneath them to the actual body sheetmetal. The rest of my bed including the underside of the rails has Line-x coating. It seems like overkill to remove the rail caps, grind away the surface rust, spray rust treatment, prime, paint and replace the caps (as I'm sure the ones I take off will not be reusable). I was thinking of just plugging the holes with some black silicone caulk or epoxy and seeing how that goes over the winter. I've seen several other trucks with similar holes that end up getting some rust around the holes where the paint bubbles up but it doesn't really become a major issue. These holes are well away from the outside edge of the bed so any rust would have a good ways to go before becoming visible on the outside of the truck. I appreciate any help!

[ManyCamaroz]

You could clean and touch up the bottom side. Dress the hole on the cap to fit a plug, shoot a little silicone in there, install the cap and forget about it.