Yes, after the delta episode, if you go back to Meteor Falls, Zinnia's grandmother will be there and she can teach your Rayquaza (even if it's a one you didn't obtain in the game) Dragon Ascent.
Source
Zinnia's grandmother
As long as it is at max friendship. Remember, affection and friendship are not the same thing! Just go ask Zinnia's grandmom to teach it to the Rayquaza you want it on. Source: Tried it with a friend Hope I helped! -It's a secret!
