I may have this all mis-understood - when "new", iron or steel is an orderly matrix of iron molecules - I think "steel" has some additional carbon molecules in there, and likely odd trace contaminants in each - results in certain strength and wear properties. When red rust is produced - is oxygen atoms that have bound to the iron molecules - when forming "red" rust, the result is a molecule that is larger than the iron molecules - often it "pops out" or is "forced out" of the matrix - have that to a couple hundred thousand molecules and you have a "pit" - when removing that "red" rust, you will be removing iron molecules - the original piece is pitted and stays pitted. Oddly, you can add more oxygen - resulting in "black" rust - which is smaller molecules than red rust - actually close to the size of the original iron molecules - often we would call that black rust to be "bluing". There is a process described on Internet called "reverse electrolysis", I think - using an electric current to turn some red rust into black rust - some museums apparently do that to restore very old metal things - to be able to read scroll work that would otherwise be lost if the red rust was abraded away.
So, removing the red rust is not going to re-fill or re-store the "pits" that were created - I have read that some people will fussily weld into each pit to re-fill it, or use Bondo and then paint over that - not sure what that does for the strength of the thing - I doubt it is as strong as it was originally? - but I do not know that.