I had a 1975 450SE that I had to completely replace the right side rocker panel (outer - there's 2 of them, an inner and an outer). What happens is the water/salt (winter here, anyway) works its way behind the plastic wheel-well guard and ends up rusting a hole in there. Water, now admitted to and sitting inside the tubular rocker section, then rusts holes from the inside out.

Also, water can penetrate from the inner panel as well (snow, water dragged inside on your feet will soak into the floormat padding and eventually rust a hole). I had a leak in the windshield somewhere that let a tiny trickle in that ended up in the rocker channel.

The sunroof drain tube also runs by the rear of the rocker, and will overflow into it if plugged.

Finally, as you've noticed, the jack tubes can get wet and eventually rust a hole into the rocker channel tube, admitting more water and the certain rust to follow. Same if you let the coating deteriorate and the metal gets exposed.

Obviously, you need to remove all surface rust from any affected area, repair as needed, prime, paint, and coat with the correct stuff, then paint again if needed for color coordination.

Old fashioned grinding is one way to remove the rusties. I've used a metal prep solution, from the local bodyshop supply house, that also does wonders.

I've had excellent results with 3M Flexible seam sealer, and various products generally sold as rocker panel coating or 'rock guard'. You can apply ordinary undercoat to unseen areas too.

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1986 560SL
2002 Toyota Camry
1993 Lexus