FE, drop it. That has no bearing at all on the topic at hand.

Anyway, how do you know that we never saw JME? We have no idea what JME looks like. It could be the organ, it could be the entire room we fight her in at the end. It could be anything in the castle. It could be outside the castle. It could be somewhere in the last room that we can't see because we can't fully explore it. Basically, there isn't enough information to form any conclusive theory on the matter.