Let’s establish what this would mean before you make your choice.
-They will be taken from their life from where they last appeared in the game. From their perspective everything they experienced has been real.
-They will never be able to return to the AA universe.
(So there’s a high risk Phoenix will never be born if you choose Ryunosuke. I don’t think there’s any other characters with actual confirmed blood relationships (Auchi already have children), but if you want to make your choice based by that together with your own head canons, I’ve nothing against it.)
-You’re going to face legal consequences if you try to kill them or do anything else that normally would have legal consequences.