The NFL has final say on who practices where and the suggestions by the Giants and Jets were rejected. It’s standard Super Bowl practice that when an AFC team is hosting the game, the AFC team practices at their facility. And the NFC team practices at the NFC facility when they are hosting. So the NFL is just following protocol.
According to the NFL, the Super Bowl teams have access to the entire building — within reason. Super Bowl teams have used meeting rooms for office space and position and team meetings with the players. They do not use the coaches offices, although the host team historically give their coaches the week off. Imagine Ryan walking into his office and finding Belichick in his bathroom.