Any suggestions what abilities would be suitable to represent knowledge of (or interest in) the Chaldean or Egyptian mysteries, Zoroastrianism, Mongol shamanism (I realize that the Mongols were essentially Islamic by the time they reached Mythic Europe), Sami shamanism, etc? Neither Artes Liberales nor Philosophiae seem a good fit, and inventing random new Theology abilities seems somehow undesirable. Note how knowledge of the traditional Greek faith doesn't get it's own Theology in AM5, either, as far as I recall; Theology is only meant for the "Peoples of the Book", I guess.
As an aside, would Dominion Lore cover metaphysical effects of any of those faiths' adherents? Especially for Zoroastrianism and the Chaldeans this seems appropriate.
That's the purview of the Mystery Cults skill/lore. Arts Liberales can be used to give the player an idea of what he's looking for, and, of course, to start looking for those hard to find or lost books that he will need to get the exps to buy up the skill.
It strikes me as a little bizarre that we are seemingly expected to treat mundane organisations as mystical cults, just so we can know something about them. But I agree, it seems the most applicable ability to use.
Mystery Cult Lore is just Organization Lore, and such is explicitly stated... somewhere. The different name is just to indicate that it can be used in Initiations. That's it. Second, there are different variants of Theology, though they all do seem to be assigned to Dominion-based religions. That's where Zoroastrianism should go. For many of the others, combinations of Area Lore and/or Organization Lore along with Faerie Lore, Infernal Lore, or Magic Lore (depending on what's being worshiped) should do.