I know that rust looks bad; but, about any car that age is going to have a little rust, here and there. The key is to stop it in its tracks. Thankfully, the fella who did the engine swap on my car also did just that. He cleaned things up and painted the underside of the car.
As for the rails, I've seen pros and cons on their impact to the car's stability in this site's discussions. I would have to think that anything like this has to be a plus toward the body's integrity. There isn't a whole lot else that gives support against its bowing in the middle. Fixing the rails with something more stiff, like some angle stock welded in place, or the FM rails, etc may be a good idea, once the car is cleaned and painted. Obviously, the engineers at Mazda saw the need for them.