In my POR 15 kit it says that you can paint directly over rust with the paint. It says the paint itself seals the rust from oxygen and moisture, thereby stopping ot from spreading.
In any case I did this in my trunk, and it looks good.
Here are some pics: (Not the rusty material seen on top of the POR finish is "left over" rust residue that stuck to trunk plastic carpet thing, not rust reoccuring after one day!)