I've never had any issues with matt paint. What makes the paint matt is an agent added to the paint which increases the surface roughness of the paint and changes its refractive index. The paint itself isn't any different, as long as you're comparing like with like. As far as I know there's no reason to believe that a matt paint should inherently be any more permeable to water than the equivalent gloss.
I'd have thought that a good paint system, well applied, should be effective at rustproofing irrespective of whether it's matt or gloss. Certainly I've never had issues with matt systems, but I have had frequent issues with paint applied (not by me) over unkeyed gloss finishes.
If it were me I would (1) get rid of as much rust and rusty metal as possible by mechanical means, (2) use an acid rust converter to make sure any remaining light surface rust is killed, (3) etch prime, (4) zinc phosphate prime, (5) primer surfacer if needed (6) guide coat then flat back if needed, (7) as many topcoats as needed