Morgana and Kayle Possible Future Lore (Fan Fiction)
This is how I personally would solve the lore hole that Kayle and Morgana are currently in.

The darkin try to become the main ruling species on another planet because their planet is slowly being consumed by the void (or slowly dying for some other reason). They develop blood magic as a way to handle the species of Runeterra because they rely so heavily on blood. Kayle is a main strategist, but never went to the front because she is the queen. Her sister, Morgana, sees the torture that the darkins are dealing to humans, and stands against Kayle. Standing against the queen and the whole planet as a single darkin, Morgana gets ripped of her weapon, which is always a tool that is very heavily connected to a darkin's soul. Now without her soul weapon, Morgana becomes mad, with the death of her sister as the only goal she can live for.
To resolve questions: I would explain the colors of darkins with the type of magic they use (meaning blood magic for Aatrox and Rhaast and definitely not blood magic for Varus) and I would take Aatrox' wings and their human-like appearance in general as a "hey, look, these 2 are similar to the darkin we know". And to explain the "only 5 darkin left" thing: There are only 5 darkin left on Runeterra. Nobody said anything about the rest of the universe.