I feel that this interpretation / misunderstanding(?) of the film's ending comes from the final shot of the three of them being together. While it would have made more sense for the story to start with Kaguya × (Teenage) Iroha and then switch to Yachiyo × (Adult) Iroha, the director and the rest of the creative team wanted the three characters/actors to be all together in the end.
I think that can easily be explained thanks to these pieces of information we have:
1) Iroha made a Kaguya body for Yachiyo so the latter can interact with her in the real world.
2) Yachiyo can make copies of herself in Tsukuyomi
With just these two facts, we can piece together the ending easily. Yachiyo probably takers Kaguya's form whenever she's hanging out with Iroha, because Iroha prefers it that way. I mean, if she didn't, why would she make a KAGUYA-looking body for Yachiyo instead of a body that looks like Yachiyo? Iroha clearly has her preferences and I assume Yachiyo would be happy to comply. But, while Yachiyo is screwing around with Iroha while looking like her former self, they need someone to take care of Tsukuyomi. So Yachiyo would make a copy / clone of herself to do just that while she's fucking around.
So that's it. At the end of the movie we see the three together because we have Iroha, Yachiyo (looking like Kaguya), and the Yachiyo copy / clone. This fits the information we have without contradicting the plot. Yachiyo and Kaguya are only one person, not two. The other Yachiyo is a copy, a clone.
last edited at Sep 28, 2026 7:24PM