What is a good clear sealant?

Agreed, Proflex is not what you use on your rubber roof, Dicor Lap Sealant is what should be used there... As far as walls go, if you like using silicone go for it. I personally wouldn't trust it, it just doesn't hold up on rv's. I have spent years rebuilding water damaged rv's and 9 times out of 10 most leaks are caused not by the type of top sealant people use, but because the trims,vents etc have never been removed to replace the dried out butyl under them. Usually the first reaction people have to a leak is to caulk or silicone the area when really the area needs to be taken apart dried out and completely resealed. An rv's top sealants should be checked yearly and trims, windows, vents etc touched up as necessary. At around the 7 year mark you need to completely re seal an rv, if you want it to last.. This means removing windows and trims, vents, access doors etc and remove and replace the butyl then re apply the top sealants using whatever makes you happy, again I recommend Proflex on the walls and trim and Dicor on the roof membrane.
In my opinion an rv is an expensive investment, why cheap out on maintaining it....