Knowing how many multiverses and magic BS there is in this series, something like this is feasible in verse.
I do wonder what the implications would be going forward in such a scenario? Aren't command seals tied to a body? Shouldn't Rider technically be the new master? Since Shinji's soul belongs in the present timeline but he's occupying a servant's body, does that mean he's kind of like Gilgamesh and now bound to the present world? Or would he still need mana from a master to stick around?