The rocker is totally non structural from the outside. Take a look at the unibody frame rail and see if that is rotting.
I own the rustiest E30 race car in the world and my body panels are separated from the car. They are just sheet metal, just like the rocker. They can be replaced.
My rails are not the greatest but as you know, you can weld to the inner rocker/floor and really strengthen up the chassis with the roll cage. That's where the structure is, and the weld along the bottom of the rocker....
If it were me, I would consider filling the rocker with expandable foam and then shave it. I would get some thin gauge body metal, and find a pal with a bender for the right angles. Make a curve after you have bent it. Tack weld, add some seam sealer and spray bomb it.
For safeties, the holes cannot permit exhaust to enter the car - it's that simple.
If a mechanic differs on that opinion, tell him to show us all where it says a simple body fix cannot pass a safety. There are a lot of swiss cheese autos on the road, and patching can be simple - but it doesn't have to be ugly.