I'm the author of one of the above posts Dave linked. I completely agree with you about Fantastic (roof) fans but I'm really more impressed with the Maxxair ones these days. I'm about to put two of them in a Transit mid roof.
There is no reason to not put a fan in your penthouse top. I have done it twice and both vans are still cruising around leak free and the tops have not been compromised. When I had the holes cut I scientifically tested the structural rigidity of the roof around the hole for the fan (This means I walked around up there and flexed my weight all around the hole and didn't fall through
) Seriously, the tops are strong. There was no more flex with the hole cut than without.
There are a few other members who have done this too. LenS comes to mind. One of the vans I did was my old van and the other was TwoGone's van. You could PM him. He's happy as far as I know.
I still don't know why SMB won't do this or approve of it but I say go for it. It is a great mod.