The situation in Port Santa is quite odd;We've never seen beyonder powers pertaining to the sea or water except for the Tyrant pathway and the fact that it's only confined around the designated part of the sea in Port Santa tells that it might be what we all know and assume to be a fact, an OD and it is highly likely that the situation in the sea might be a mystical item gone rogue; it could also be both MGOD has been in control of the half of the church, it might be that she's colluding with this OD in preparation of the upcoming Apocalypse.
Considering how Noelia is from the justiciar pathway and how she’s always mentioning trying to maintain order, I wonder if there’s some influence maybe from the night emperor that causes them to not interfere, afterall the night emperor was married to Auernia who should’ve been very connected to Lilith at that time