Having grown up in the rust belt and moving to Texas and now Arizona, I can not stress how much easier the hobby got dealing with rust free vehicles.
With that said, a repair like that is just not cost effective or practical to do "right" with new metal. If it was mine, I would either sand blast or use rust converter on the area, paint it, use several coats of seam sealer or urathane to make sure it was water tight, paint it again and go forward. I don't like fiberglass or tiger hair because those products tend to corrode the metal worse over time if not properly treated first.
I understand wanting to do the best repair possible, I'm like that also. Sometimes it's just not practical and stalls the project over something that nobody is going to see and it just has to be water tight.
Just my .02