Genetics. If a certain scale color is dominant or recessive, and the genetic code for that scale color isn't in one of the tribes (e.g. Raen don't have a genome capable of expressing black scales and vice versa), then it won't be possible for that tribe to express the opposite scale color. There's also the possibility of co-dominance, meaning the colors mingle together and produce a grey scale coloration, but inter-clan relationships are rare and undocumented. Without scientific study, it's impossible to tell.
While the Au Ra aren't the only ones to exhibit sexual dimorphism, they are far and away the most extreme case. Roegadyn females just don't have the muscle mass the men do; besides that there's very little difference between the sexes of any race. You wanna talk environmental adaptation? Well then, the Roegadyn Sea Wolves should have webbed hands and feet to help propel theyselves through the water for when they fall overboard, and not be anywhere near as massive as they are unless they regularly haul up large sea game to feast on.
... but it's just a game, so whatever.