There were two main factions that controlled the Moon Tribe's culture: Science and Magic. The science faction was supported by the military and most politicians, while the magic faction was the clergy and most intellectuals. In the middle we had the Royal Family, who couldn't side with only one faction because both were powerful pillars of society, but they still kept them separated and not stepping on the other's toes.
This was particularly awful for the magicians, who had discovered by clairvoyance that the scientists were playing god and creating nasty weapons, and summoning all kinds of evil creatures. They knew that this would bring the destruction of their land, but sadly both sides had the same technology and any fight would end in a draw. Besides, the laws didn't allow them to stop the scientists anyway (plus they knew the end of their world was fated and they didn't fight against destiny). So the plan of action of one of the elite monasteries was to focus their resources in the post-apocalypse, ensuring that the shit that the scientists were unleashing wouldn't destroy the other worlds afterwards.
That said, in my headcanon Waka belonged to that monastery as an acolyte. He was the best prophet of them all despite his young age, and he always knew that he'd be the only survivor from his order. He has visions about most of the nastier demons and he trained himself a lot in magic and martial arts to increase his chance to live through them. (Also, the Tao Troopers are slightly based in these monks.)
But that said, the THEY that made the Trojan horse that was the Ark of Yamato were a branch of the scientists, who realized they were doomed a little too late and their solution was to seal their mess and dump it to space. Waka sneaked inside as a stowaway without knowing what that ship was.
Meanwhile, the THEY that were involved with Kurow was the higher-ups of the Tao order, not the scientists. They created the doll of their best magician as a living seal for Akuro. Waka did know about the doll, but he was kept away by his superiors and he didn't realize the little guy had feelings. Besides this happened when Waka was still very young and he was just following orders and his own prophecies without questioning anything.
And the third THEY, the ones who shipped Deidarabotchi, who were a less douchy/evil branch of the scientists, and tried to get rid of some of the worst weapons of mass destruction they had invented so no one would use them. Sugawara was a noble who was a part of this group.
And then there's Kaguya, heiress of the throne, who has nothing to do with any faction and ended up on Nippon after her parents successfully pulled a Superman origin.