So, regarding this "Rainbow Rocket" alliance thing (is it confirmed in any way?)... given that Solgaleo/Lunala Poke-ride is postgame, might this be an actual explanation for finding the legendaries, rather than just being Hoopa Solgalunala-portalled in? We know Mewtwo's in, Lugia and Ho-oh are probably in and the prominence of the other generations' cover legendaries on that national dex booklet might imply that they all show up.
If the team leaders' plans were successful, in most cases that would involve stopping the third version legendary from interfering -- possibly by capturing it. And in previous paired versions, the team leader's plan has differed primarily by which legendary they care about. So it kinda makes sense if Rainbow Rocket goes slightly differently by version, and each team leader has two ubers that you have to fight (which would make them very threatening postgame opponents). They lose them on defeat and the player can then go and catch them.
For instance, Ultra Sun might have Maxie with Primal Groudon and Mega Rayquaza, Cyrus with Dialga and Giratina, Ghetsis with Black Kyurem and the Reshiram he took from N/the player, Lysandre with Xerneas and Zygarde and Giovanni with Mewtwo and Lugia. (No real reason for Giovanni to have Lugia or Ho-oh other than fanservice, admittedly.) Ultra Moon would have the corresponding opposites, and this would explain the version exclusivity of certain legendaries.
Obviously this is wild speculation, but if that is the explanation for the presence of legendaries like Mewtwo in wormholes, that means we might not necessarily get all of the VGC relevant legendaries -- they're much less important to the plans of the teams.