Agreed that the scars are an important detail and probably a clue about Cowl's identity, I just don't think he's Kemmler. And recall the conversation he has with Harry, where he states, "I don't perceive myself to be mad." So he spits on Kemmler's name and calls him a madman, then later claims he doesn't think he, himself, is insane.
Only possibility I can see is Cowl not realizing that he was Kemmler; too many bodyswaps left his personality in flux until he became Cowl, and perceived Kemmler as a wholly different, and abhorrent, entity.