The whole point is that Khan is supposed to be a super-genius, Wily Coyote-style. If he's so smart, why would he say something as stupid as "behind the aft nacelle"? Why doesn't Spock react to his blunder? And, for that matter, if he knew where the life support system was, why didn't he destroy it with his opening salvo?
Answer: Because the film makers don't care about any of that.
What opening salvo? Khan fired on the Enterprise only after he got his people back.
He clearly wanted to avoid shooting at her for fear of putting his crew at risk when targeting the life support system.