Pretty much. As long as continuity of consciousness is maintained somehow, engram V is the same V.
I don't buy Johnny not being a fully conscious separate entity though, mostly because of Misty's attitude towards him and the Zen Master talk about two souls in one body.
I think the truth is something in between. Johnny is a separate entity(he'd have to be to get disentangled in Mikoshi) , but the hallucinations are your brain struggling to process two personalities.