Never understood why some of those northeastern states like MA and PA get so excited about a bit of rust on the outer skin. The state is the one who puts the salt on the roads and then make a fuss when it eats the skin of your vehicle. I could see failing a truck for brake line, body mount or frame rust, but holes in the skin never hurt anybody. There are literally millions of cars on the road with rotten rockers, cab corners, and rear wheel areas. They don't explode or fall apart on the freeway. It's easy for some millionaire state politician to pass laws against ugly. He/she never owned anything old.
Like you said some expanding foam and fiberglass hides it and passes. Yet that doesn't effect making the body any stronger.
After doing the repairs "Rust Wrap" it. Like the all fiberglass bodied Corvette below. Wonder what the inspectors would have to say about this one. We all know fiberglass bodies don't rust. Would it pass?