The thing about rubber is that it is so thin, it can get a hole punched through it very easily. Combine that with the fact that the seals are at corners that get wind (which is almost like a pressure washer action), and it is no wonder why it is only a matter of time until a RV with a rubber roof self-destructs.
My ideal roof would be one piece aluminum that is "cupped" around the edges and corners, so water getting in past a seal on the sides of the rig doesn't mean an instant leak, unlike rubber roofs. Then the items on the roof are installed (A/C flange, skylights, vents, etc. Finally, the entire roof is then masked and sprayed with an epoxy based elastomer sealant (rvroof.com, Rhino Linings.) The result would be a one piece roof with no need to worry about caulk or Eternabond, and even if scratched by a tree branch, the roof likely will still be watertight unless the branch punctures the metal or knocks a vent off.