PlanetTraitDefs.xml decides the class for special planets.
The only other place is (as you mentioned) in GalCiv3MapDefs.xml, which I'd expect to be regular planets - nowhere else does it specify the planet class.
And indeed, if I change the values in GalCiv3MapDefs.xml (eg, making the higher class planets more common), I successfully see that in-game. (but only on non-special planets)