In my experience, it is not just the holes that are causing the rust, it is much more the fault of condensation and poorly protected metal on the inside of the rocker. The poor coating is added before the panel is welded in place, so the spot welds become areas for immediate rust.
If you get snow caked on the rocker, and warmer air inside, you'll get water beads forming inside = rust.
Solution: as soon as you get a car, use the existing holes and adding holes if necessary to spray in oil based substance to coat the interior. I use CRC brand white lithium spray grease, WD-40, or similar with the tiny red spray straw to spray inside the rockers and fenders.
A totally easy spot to reach is on top of the wheel arches thru the trunk area, just pull back the liner or remove the plastic and spray on top, or use a brush to apply grease.
Again, I really think its the condensation that occurs, not the few holes here and there in the rockers.
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