Personally, I don’t like a dark fantasy storyline without a plot twist, or one that’s monotonous or absolutely grim without humor or details. It feels rather pointless. There are still quite a few ominous points in your analysis. I lean toward the idea that the Father is a good person, like how the elder women behind the village alley said she used to work or enjoy something wonderful at the church before the bridge collapsed, and it felt like the church abandoned the village, but it was the other way around. At the very least, the focus of both games’ storylines should be Rabiance, Lelia, and the monster, not another figure like the Father. So, I believe the Father is good. That said, I can’t completely dismiss your opinion because there’s still a possibility that he’s the mastermind.