Maybe he's pre Hartnel and is the real first incarnation of the doctor. Maybe he was a real ass hole before he reformed and became the doctor. The tenth doctor in The End of Time stated that "I've taken lives before, convinced people to take their own, and worst I got clever" or something. Maybe he's either referring to the pre 1st doctor or 8-9th doctor. Either way, I think he's probably talking about Hurts "doctor".
Maybe he was the Valeyard before the Doctor, and in his thirteenth incarnation or whatever, changed back. Maybe the Valeyard his the Doctors true nature he keeps buried beneath himself.