I think that I would take the worst of the rust off with a wire wheel and then coat the remaining rust with a rust-killer available at auto paint supply stores. The one I have is called Rust-Mort. I am sure that there are others that are just as effective by a different name. Then two thin coats of bed liner from a spray can should protect the surface and quieten the road noises that are sometimes amplified by fender vibrations...JTL
Rusteco also works good.
Avoid the bedliner approach. All it's going to do is to provide a place for oxidation to keep occurring. If you get a pinhole through the other side and subsequent water ingress, the process will accelerate. The rust needs to be chemically neutralized then stopped by virtue of a metal sealer - NOT a paint or coating.