Atemi can be used at the end of any technique, once concluded, or concluding. Doesn't need to involve the use of knife or short sword, mindset wise. Palm heel strike to base of skull or knifehand edge to larynx are darn near as bad.
Thing is, if you practice kata as you want to "use it," if you do end up using it, and there's only the one "bad guy," and you train that way .... it's likely that you might finish that way, thus killing/maiming your attacker.
That being said, think about the post-attack ramifications on "defender." You had him controlled, he was at your mercy, and THEN you chopped him in the neck.
Therefore you killed a helpless person. Therefore you just, according to the law of many (perhaps most) jurisdictions, you just committed at least 2nd degree murder.
Just something to consider while you practice kata. What you practice is what you'll do, most likely.
Koryu jujutsu, Daito-ryu, Hakkoryu (to refer to a few arts within the family tree of aikido) all include many waza/kata with ritual finishing "killing" strikes. Based on my experience, however, the flavor of such techniques helps instill a gravity in one's mindset conducive to addressing a violent or potentially violent encounter, vs. resulting in literal, rote execution of a given technique.