Since we're talking about Lusamine, what about the screenshot on 4chan that depicts her together with Lillie and the others seemingly normal?
If the story from Sun & Moon is of any indication, shouldn't she be unconscious at this moment of the story?
Of course, the legitimacy of the screenshot hasn't been proven yet, but to me, it looks extremely detailed to be a fake....
If it's true, then I can see the story going like this:
The URS comes into the Pokèworld in order to take custody of Cosmog and bring it over to Ultra Megalopolis, but Lillie finds out about their scheme and escapes from Aether Paradise.
The URS starts travelling around Alola by following traces of Ultra Aura and we've got confirmation of this by Phyco himself.
Due to this, we will probably be meeting them a lot during our journey, which justifies Lillie keeping Cosmog in her bag all the time.
All of this until we will reach the Altar, from which the climax of the story will start.
After Necrozma's appearance, the URS will decide to join forces with us in order to capture Necrozma (As shown in the trailer and the infamous screenshot).
Then again, there would still be the problem of Type: Null....
Of course, they could say that this time it was Faba's will alone that made this Pokèmon's creation possible...