Pitted roof from rust under vinyl top repair

I'm not surprised the POR15 didn't seal it. You cannot just paint over rust, it will return eventually. You have to chemically change rust with a rust converter and then you can seal it with a product such as POR15, Rustoleum and the like. You have to change the rust on a chemical level. I would treat that whole roof with a converter and then choose the sealer of your choice. Either that, or put a roof skin on it.