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Although they regarded each other as heretical sects that must be eradicated, both Ymir and the Orthodox Church were means and agents used by the Mother Goddess to interfere with the Wisdom Species, akin to a company's finance department 1 and finance department 2, while the Divine Agent can be seen as the practical executive branch. They collaborated with each other, constituting important forces in the system through which the Mother Goddess interfered with the world. Therefore, it's not surprising that the highest hierarchy of the Church has one or two channels to contact the Mother Goddess.
What could be considered unexpected, was the Divine Agent.
