Had the exact same type of paint problem on the door of my 2009 Adventurer. I had the door repainted when I had some other paint work done. I never seemed to get any worse and hasn't returned after the repair.
You may also want to check out under the MH especially the metal tubing that supports the basement storage. There is a big problem where (in my opinion) the metal wasn't prepped correctly.. Every year I have a bit more to sand down and re-paint because it is not necessarily rusting but the paint is pealing off.
As far as re-sealing the roof... Yes on Winnie's that is a major maint. point. The roof is really held on by the sealant and it is NOT SILICONE. NEVER USE SILICONE on that joint.. it will fail. You need to use the Winnebago recommended sealant. To do the job right you have to dig out all of the sealant and reseal were the fiberglass roof panel tucks into the drip edge. 2 years ago I had it completely re-done ** the whole MH** to a tune of $2200.00 it is very labor intensive but at the time I had the MH pressure tested.. you would be surprised how many leaks there were.
2009 Winnebago Adventure 32h
2006 Terry Quantum 330FKDS (beach getaway)
2003 Aprilia Atlantic 500
2007 Honda Reflex
2 house rabbits "George and MiMi"