Why is the Green Sun green? If Universes A and B are red and blue then green is the complementary color there, but that raises the question of why they're red and blue. I could maybe see some association with Calliope's blood color, but she had no role in its creation. Is there even a reason for it at all? I know you've mentioned a red vs green theme before; is that somehow involved?
Honestly? I think it’s just color Palettes. It would be the same as asking why Rose’s Land is focused around the CYMK palette. Colors hold a lot of Symbolism in Homestuck, but sometimes Colors are just like that to be thematic, I feel. First Guardian Spacey Powers are Green, so their Source of Power has to be Green. RGB palettes are thematic, Red-Blue is a good duality, so the Universes are Red and Blue, and their detonation makes the complementary Green, which ties to the First Guardians. It’s thematic, but a lot of it also feels like Retroactive Foreshadowing, you know?