You need to accept there is no real way to paint over or encapsulate rust. Not with these products. There are corrosion control primers found in various industries, and they are effective. They are also expensive, and often times quite toxic.

There are rust converters that work by converting iron oxide to more stable magnetite chemically. The downside is you can't control how deep the conversion goes, and you cannot control adhesion on either side of the conversion.

Your best options are to remove the rust and treat the metal. There are acid based rust removers that are effective, such as Rustmort, Ospho, various PPG products, and others. Can be nasty, use precautions. And they must absolutely be neutralized before being coated.

There are chelation agents sold by a number of companies, Rust911, Evaporust, and others. Very effective, non toxic. Extremely slow. Can get expensive, but re-using the solution helps make it economical.

Mechanical rust removal is an option, but on thin sheet metal may not be practical. Grinding, blasting, wire wheel, etc. Could combine with other methods to form an effective plan.

Note, real epoxy primers will have chromate. This will allow the epoxy to adhere to metal that may have microscopic rust in less than perfect areas. This is helpful, but not a substitute for rust removal.