If Genesis is logic and Exodus lack of logic, then trying to deduce whether Hanemura is the prince of Exodus is futile. If he seemed like one, he might not be one, because it would be a logical outcome. It makes sense Genesis would try to control events (sensibly) to further its own agenda, but Exodus would rather cause confusion to drive its needs in a roundabout way, just like Samon and what's-his-name were blathering.
Still, it has been nice to think Aika was the agent of Exodus. She surely was enjoying confusing Mahiro and Yoshino.