Coriander: All of this seems fine! There's no requirement to rewrite the plot NPCs, as Phantasmal Rift works strongly on multiverse theory. As for her Pokemon, she could bring either her sentient companion or a normal team of Pokemon.
Nathaniel: I'll say the same rule here for Zapdos; he can bring the Legendary or a normal team, and must get the other through regains. Interaction with Legendaries is fine, as they're the same as any equivalent godlike NPC in another canon.
As for their PTU system powers, I have no familiarity at all, and would need you to go into more detail!
whoops this is late I'm sorry
Nathaniel: I'll say the same rule here for Zapdos; he can bring the Legendary or a normal team, and must get the other through regains. Interaction with Legendaries is fine, as they're the same as any equivalent godlike NPC in another canon.
As for their PTU system powers, I have no familiarity at all, and would need you to go into more detail!