I cheesed him like I did with all the other stupid ninjas in the game: long trap chains starting with a spark rod at the door. They can't backstep from there, and if you trigger early they won't blink either. Rake works too, but it's less reliable.
Or if you're feeling adventurous: if you stand in melee range he tends to not throw knives, so you can bait him to a trap by walking slowly towards it then dodging his attack.
I wish I read this earlier, I used auto-defence and it's been surprisingly easy, it's so OP.
I'll try the door trick next time.