Got a plan for that first part already, during Chapter 7 the MC will have to go through an Ultra Wormhole, there will be an Alt Universe girl version of him who has those kind of powers, she's breeding all the MALE Legends in her universe.
Never really thought that the birds were that far from Lugia, Kanto and Johto are right next to each other, when you can fly it's probably no big deal to hop from one to the other.