I had a Thule 'Weekender' mounted on my roof of my truck camper. Worked great. What I did was mount with carriage bolts thru the ceiling and roof to a C channel bar. (the kind used for supporting A?C units in buildings, can't remember name for it), then using the spring nuts for it, bolted thru the Thule into them. Had it up there 5 years, no leaks no loose no problem.
As mentioned, seal it good.
Winnebago does have F/G roof, but still mounted over trusses. Pay real close attention, maybe write to Winnebago for placement and you can do it right. No matter how you do it, don't store the cock collection up there, makes good storage for extra chairs, a bike, other light stuff.