I think they mentioned something about this in the extras via Showtime that they've changed the 'direction' of his father's figure in recent seasons. They started in Season 3 - his father is appearing to him as he would look if he were still alive rather than as the man that raised him.

I too think Dad has become the Dark Passenger. Dexter could, theoretically, be 'normal' if his dad wasn't there to egg him on.