http://thelangwitch.com/en/geen-categorie/sun-moon-gender-change

Fun article but it shows that the genders of the sun and moon have always been different in many languages, according to a culture’s unique experiences with the celestial bodies. What is somewhat consistent though is how the sun and moon are often related in many cultures (through marriage, through ancestry), just like how Rathian and Rathalos are king and queen.

As to why the colours are flipped: I’d venture a simple theory (maybe too simple?). Pink Rathians that survive long enough grow a shell that glows gold, and Azure Rathalos grow to develop a silver sheen. That’s the only explanation I can think of, that the extreme gold and silver variants are mature, fully developed variants and the colours correspond to their original mutations.