Yeah, just like Nantara's additional notes – while it's easy to assume that Takamagahara where the amatsukami came from is the Lunar Capital, the way the narrative is worded in Yuiman's bio seems to suggest that they're separate places.

The Lunar Capital seems to be a place where gods who don't like impurity may migrate to. Remember, Jōga (Chang'e) is Chinese, not Shinto. Perhaps we can find gods from various pantheons there, just like how there are various yōkai in the sanctuary that is Gensōkyō. Maybe Hecatia's grandma Phoebe is a Lunarian.

And not everybody's there, it seems. Konoha and Ariya are back on Earth. And Ōkuninushi and Takeminakata are sealed in shimenawa?