I said franchises, not independent collaborations
Dont worry about that. Besides, here is a fun fact that all of you should know:
Chihiro Fujioka is the Lead Director & Developer of SMRPG, Lead Developer of Alpha Dream; (which is owned by Nintendo) & Lead developer at Square Enix!
Shigeru Miyamoto was also the Producer of SMRPG
Hironobu Sakaguchi is a VERY POPULAR game designer, game director, game producer, AND IS THE CO-FOUNDER OF SQUARE ENIX! He is famous around the world as the creator of the Final Fantasy series, and has had a long career in gaming with over 80 million units of video games sold worldwide. He was the production supervisor of SMRPG. He is a close friend of both Chihiro and Miyamoto.
They are all literally responsible in creating the content of the game.
Bottom line: It isnt the company itself that has a say if geno gets in. Its all up to Hironobu Sakaguchi. And knowing him, I definitly see Geno already playable from the start of the game's production