Never heard of having to remove the cap to fix Winnebago rust problems. The windshield has to come out, of course, but you should be able to clean up the rust areas once it is out. Do you suspect a water leak somewhere above the windshield frame?
Have you called Winnebago Customer Care to discuss the problem - they should have some useful tips and maybe even a recommended procedure. Sadly, it is a fairly common problem on Winnies.
2004 American Tradition; 2014 Buick LaCRosse
Homebase in the Ocala Nat'l Forest near Ocala, FL