Sorry for the thread bump, but, holy hell do you guys give some bad advice when it comes to body work!
The RIGHT way to fix those holes would be to weld them shut. There really is no alternative. You don't use metal tape and bondo to patch holes. That's some hack-ass backyard BS that gives the hobby a bad name.
You ESPECIALLY do not bondo rocker holes. Bondo absorbs water like a sponge. Even if you put metal tape behind the bondo so it it was "sealed", metal tape is nothing but ever-so-slightly-thicker tin foil that can tear at any moment.
The OP mentioned wanting to keep the holes in place in case a buyer for the truck wanted to reattach the boards. That's fine, especially being in California. Dab a little paint inside each hole to seal up any bare metal and use friction plugs/Christmas Tree plugs, similar to the clips that hold most door panels and fan shrouds in place. You MIGHT consider adding a dab of silicone to each plug to hold it in place and prevent vibrations from rubbing more paint off.