While it is possible that Rossi could have his own setup, I doubt it would be a VR46 branded Team as he has been quite clear that the VR46 academy and Team are for bringing up and coming Italian riders into motogp. But yes, anything can happen.
No way would he have a VR46 branded team yet as that is somewhat his trademark for his business and other teams but he could be part of a team that 'evolves' into the VR46 branded MotoGP team when he chooses (that is my thoughts if it were to happen).
My personal suspicion only is that he will not ride for a VR46 team anyway but will be the figurehead but I could see something along the lines of the old Nastro Azzura days with a major sponsor looming large on him.