I'm on board with the theory that the Raps are future humans. Maybe they come from a future where the earth is a wasteland due to humanity's mistakes (war, pollution, whatever), but they've invented the technology for time travel, so the survivors travel back in time to correct their mistakes. But they don't trust present-day humanity to change willingly, so they conquer the earth in order to force the timeline to change through fascism. It would also explain why they have that "Rolodex" on everyone, and knew exactly who to target on day 1, since they come from a time where everything up to the Arrival is history to them. Since the Arrival would be the point of divergence in the timeline (or slightly earlier than that, since Snyder implied that they came to him a little before the attack), everything should be the same up until that point.
Also, maybe the Raps have purposefully cultivated the image that they are aliens, in order to throw present-day humanity off the trail of who they really are. Putting the Factory on the moon, having elaborate demonstrations of things launching into space, all designed to hammer home the point that they're from another planet. Because if the population figures out that they're really future humans, maybe that knowledge alone could alter the future in ways that are undesirable to the Raps.