So gonna take a random guess, the part about how humans are the superior beings when they open thier third eye and transcend part that the church found out about and here of from thier 'Pope' gonna take a random swing and say that cause this series is taking quite heavily from lovecraftian lore that the so called god that the church is in communion with through thier Pope is nyarlytotep or that the Pope is actually nyarlythotep. My reasoning for this is it takes form lovecraftian lore and has already named one of the old gods as cthulu one that is apparently the epitome of evil, it would make sense for the god that controls the church from the shadows be nyarlythotep as his whole gimmick is manipulation to bring the world to the brink of destruction for it's own amusement and it usually did this through manipulation of church leaders and or powerful figures in history to make them think theirs was the just way.
But yeah anyway my two cents could be very wrong but all I know is I came here for trashy isekai and I got lovecraft disguised as trashy isekai so going by that and the way the church acts and operates imma say the person pulling thier strings ain't that pope its nyarlythotep, which makes me want to see some of the other old gods now