But isn't that just semantics? At the end of the day, Hurt is the ninth incarnation of the physical being known as The Doctor.
Except that he specifically requested to be regenerated as something other
than a Doctor, and the Sisters (using their somehow "elevated Time Lord science") granted him that request.
He might still be the same physical being, but it seems pretty obvious that (at least by Time Lord standards) he had become something slightly different and separate. Otherwise what was the point of the minisode? Just to have the Doctor delude himself into thinking he was becoming something different when he wasn't? I seriously doubt that was Moffat's intention behind the whole thing.
Clearly he wanted to use the Sisters and their magic to make this a very different
kind of regeneration.