In my honest opinion, references need to be put in very delicately. Now, I'm mainly saying this because I've never played a Persona game (blasphemy, I know) but as others have said, once you start placing in references into a game with high levels of gusto, you end up making a standalone game in a way. Now, if the was a separate game based off of these, I would be all for it, but in Reborn, I believe the references need to be done very finely, like the Miku reference or the JB character.
And of course, it does all depend on if Amethyst has ever played the game too. That's kind of a deal breaker, if you ask me.