Got the Conqueror's Crystal!
It only activates in Nobunaga's episode and Nobunaga, Mitsuhide (his episode needs to be played first to unlock his transformation), and Ranmaru are all Level 2 and do something in any place together (though I did it in Dragnor). It's not really necessary to have them at 80%. Zekrom will appear after doing anything in any kingdom while Nobunaga has the crystal equipped.
That's enough clarification, I think.
EDIT: Oh, screw you, game! I have to go through the MC's episode again just to get Shiny Rayquaza.
(Serebii, would you please update all related info? There's NOTHING in the legendary page where it says Rayquaza appears in Two Heroes of Ransei.)