Surface rust is most often a function of exposure to environmental elements and is more commonly known as "industrial fallout". Your present issue is inner door surfaces. Industrial fallout will never be an issue causing "surface" rust on inner door surfaces. Of course, I don't know your history.
The only real possible rust failure you might see is failure of a non-painted surface or the door not properly draining water resulting in corrosion. On mine, I didn't see any non-painted surface or draining problem. If the dealer paints the surface, he will have to prepare it so it adheres..... sanding etc. Down the road this repair could cause problems. Understanding this, if it were mine, I would do nothing but ENJOY THE VEHICLE and keep a copy of the dealer's repair order noting the concern "in file" for future Ford consideration should a failure occur. They do consider documentation like that.
From what we've seen, all other Edge doors show a similar condition so it's how it's built on all vehicles. A replacement door would not improve yours or my situation.
What does the dealer think about the issue? What would they do if they had the issue? If the vehicle were theirs? Ask them! Dealers will do a lot to satisfy you when you believe you have a concern (you are upset) but would not do the same to their own vehicle because in the long term they believe it may not be the best solution.