Samus and Falcon have worked together, but Jay and Isabelle have yet to meet in NinTheGame. Remember, the human brain is being used as a conduit for an upgraded AI, where both the character and the person share memories. Captain Falcon and Jay are different people, but for all intents and purposes they share a mind atm. Think of it like the relationship Rick Jones and Captain Marvel (Mar-vell, not Carol Danvers) had in the old Marvel Comics.