NCPinz--
I won't be of much help on this issue, but will pass along my thoughts as requested.
First of all I'm going to assume that you're getting an "overheat" shutdown code or are otherwise confirming the shutdown is due to engine overheating. The Onan shutdown problems usually relate to fuel in one way or another.
I actually think the Phoenix statement you noted is largely accurate. I've monitored this forum closely for six years, and read a lot of the old posts prior to that. I really don't remember an engine overheat issue with the generator surfacing to speak of. There have been a lot of generator shut-down discussions, but they normally track back to some form of a fuel issue. There have been suspicions of vapor lock due to heat--but that (if it occurred) would again actually be a fuel issue.
I personally have never run my generator with the access door on the PC open, and I have operated it in some pretty warm conditions (I live in Oklahoma). I have also on a few occasions operated it for a substantial period of time (hour or two) while sitting with the Ford engine running in hot weather with no noticeable issues. Also, again, I don't really remember any forum discussions of PC owners needing to leave their access door on the side of the PC open. Of course Onan warns against operating the unit with the generator side cover removed--it is specifically needed for proper cooling while operating.
I'd be interested to see what Onan has to say, if your service guy gets a response from them. Please keep us informed of progress.
Thanks, Mike