Thanks for the warning.
I thought about that. There are a few guys here with side skirts on their cars and they've had them for quite some time - they don't seem like they have any accelerated rust issues. But then again, they have yet to take down those skirts to inspect the sills. And also, I think that rust forms from the inside of the sills rather than from the outside, moreover, the outside is heavily coated with the stone guard. Thus, the rocker panel covers are effectively resting on that thick layer of stone guard and not on the metal. If there's any rust that's going to form, it's going to be from the other side of the metal, or in between the stone guard and the sill. Hence, the trim panel shouldn't have contributed nor have anything to do with that rust formation. If any rust formation should occur it would probably form at the drill hole, of which there's only one on each side - no more than that which is required for side skirts.
Yes, that accelerated rusting might occur does bother me, but that only means that I should be a bit more vigilant in looking out for it.
Again, thanks for the warning.