Nah, you haven't missed anything. As with uh... most of KH3's ending, I don't think we're really supposed to understand yet. We know Chirithy doesn't "work like that," but we don't know precisely how it does work, or exactly how the Final World works for that matter. For now you can speculate, but you'll just end up with more questions. It's a mystery that'll be explored later. Maybe in Melody of Memory? I hope?