So the conclusion you're drawing here is that the black eyes are specific to Kabuto's mind controlling Kunai?
I don't know if it's the same in the manga, but the first time they showed Kabuto doing it with Deidara on the turtle island, Deidara's eyes were completely black, then Kabuto inserts the Kunai and Deidara's pupils reappear. So, again, this seems to imply that the black eyes have nothing to do with the kunai.