Start with what we actually know — because this theory is built entirely on facts the game already gives us.
Fact one: Idrila, the Aeon of Beauty, disappeared one day. No warning, no explanation, no body. The galaxy's official record simply says THEY "vanished" — exactly as mysteriously as THEY first appeared. Their followers split over what happened: the Mirror Holders insist Idrila shattered into relics, while the Knights of Beauty refuse to believe their Aeon is gone at all.
Fact two: Pom-Pom appeared on the Astral Express out of nowhere, sometime after Himeko repaired the train. Ask about their past and you get a polite dodge: "Pom-Pom is Pom-Pom, your respectful conductor." Nobody aboard knows where this creature came from, what it is, or why it devotes itself so completely to the passengers' happiness.
Two unexplained disappearances and appearances. One missing god. One mysterious mascot. What if they are not two mysteries — but the same mystery wearing a very cute hat?