Kurt,
I think in most cases it is not the paint, most all the automotive finishes are very durable with the exception of some peeling clearcoat that sees excessive sun light on our roof edges. I believe that is somewhat driven by inadequate coverage applied there and possibly some prep issues given it is the same clearcoat used on the sidewalls that holds up better.
There has been some reformulation of the resins used for fiberglass and not all of these appear to have been durable. I have a friend with an Allegro Bus that went back to the factory with that issue on a roof and they pulled the whole fiberglass roof panel and replaced it. I have no idea how many coaches they have done that to or how pervasive the problem is.
Unless it causes real problems to the sidewall resulting in delamination issues I would probably live with it, if not trade the coach for another.
In the marine industry fiberglass boat bottoms had the same blistering issue and there have been barrier coats created. The procedure was to sand any paint off to bare gel coat and apply the barrier coat, sand and then apply paint. Whether that process could be applied and then the coach side primed and repainted I am not sure but it would seem likely. It would be an expensive experiment. Perhaps the factory in Red Bay Alabama has more extensive knowledge on the issue and maybe they have a process to repair and reuse those panels they have removed.
Later Ed