Well, the phosphoric acid actually dissolves the rust, and it washes away with the rinse water - if it has been in contact long enough. That's why the commercial rust removers have a 'thickener' added, to give the acid time to do its job.
Scratching as much of the rust as you can out of the pits before applying the acid also helps, but it's a tedious job if there are a lot of them.
Those epoxy products are quite viscous, and very suitable for filling pits, but not as an overall coating. It's simpler just to swab the whole surface with the acid after doing the pitted areas - as soon as it turns grey, it's ready to rinse off, dry, and hit with a primer coat.
