I like a wire brush on a drill for areas like that. A wheel style for large areas. A cup style for smaller areas. For hard to reach areas you can try steel wool/navel jelly. You can also knock off the loose stuff and apply POR15 or Rust Encapsulator or similar product of your choice. It took 30+ years to get that small amount of surface rust on it. With a little elbow grease and some POR15, it'll last a lot longer than you will.
I'm not so sure about the rusting thru byu the looks of that. I'm no expert, but I had removed the headliner backer etc in my car and over time it had gotten rusted, kind of like the looks in the pics, but not bad at all really - no pits or deep rust, just a fuzz like from condensation on the roof. I was jus lookinn at it last night. On mine, I'm thinking about some of those 2-3" pads that are for cleaning, then epoxy. I know people have used POR15 but the more I read about it, the more I don't want to use it - never have. I think now, after having spoke with guys who swear by epoxy that it's just your best bet. Maybe one of those Pro guys will tell you what to do, and as importantly, what not to do.
I think the question is: how clean are you going to be able to get the metal first? It's my understanding that epoxy (or any other basic paint) over any rust (surface rust, pits, etc) will fail with time. If you can't get rid of all the rust, I wouldn't cover it with epoxy. Similarly, I don't apply POR15 over pristine metal, that's not how it's supposed to be used. Fortunately, that area won't be exposed to much moisture so which ever way you go, it's not likely to cause much problem in the future. I've never had POR15 fail me when used appropriately but I don't like painting over rust. I'd get rid of whatever rust you can. Whatever you can't get (in seams, in tight corners etc) I'd dab on POR15 before it dries completely, mist the POR15 with a quality primer and topcoat everything with whatever product you want. To be honest, if you get the metal real clean, a spray can enamel should provide adequate protection in that area.