I have seen mopeds on hitch-mount racks with horizontal troughs ala
Hollywoord or Sportracks. I doubt if roof racks would be strong enough
unless you really strapped the hell out it with ratcheting moto straps.
If you rack system is burly enough it would be better to lay the ped on it's side.
If you let the air out of the tires they WILL squeeze into the troughs. I have
had my downhill MTB on a roof trough with 2.8" Michelin tires, but even at
only 45 lbs it was unstable without straps.
It gets ugly when a roof mounted bikes falls over, for the bike and car
-seen it happen. I say throw a packing quilt up there and lay it down.