"Epoxy" is a thermosetting synthetic polymer containing at least one epoxide group in the molecular structure. Essentially, you take two chemicals, each of which contain part of the final molecule in some binder or carrier fluid, mix them together, add heat and voila! they set hard into a mass. They are used as paints and coatings and adhesives in a wide variety of applications. *Why* this is done can have many reasons.
I am not sure what you mean about what kind of magnets are used in other mods. The kind of magnets used are "rare earth" magnets, usually neodymium. But I think you probably mean "non-epoxy coated" magnets, that is bare metal. I happen to have a couple of mods with magnet doors and the magnets are regular old metal colored ones.
As to whether or not they are better, it would depend on for what purpose. In engineering design, better or worse, by themselves, are pretty meaningless. It's about "suitability for the designed purpose." The magnets in the mods you mention might be expoy coated for some specific design reason. Electrical conductivity has been mentioned, but there are other purposes possible: a slicker surface to make them non marring, or easier to clean, for example. It's also possible the main purpose is advertising, or cosmetic.