For me Ground Zero and The Phantom Pain are the same game. My assumption about the sequence on Phantom Pain is possibly a flashback to 1972 when he was in a coma and The Les Enfants Terribles project was created. Thus the missing arm. The whole dreaming effect he is having could be Psycho Mantis (Or who ever the floating character is) doing.
Human Instrumentality Project
Sacrificing older life to create a new lifeform blessed with the fruit of life