I would definitely take her from AFTER Ni Akeria, especially considering the scene she has at her shrine. Taking her from so early in the game alienates people from apping characters whom she won't recognize yet, you can hardly call yourself a castmate. It makes it awkward for potential other people. A later time point (maybe after arriving in Cahalla) would work so much more in the players favor in my honest opinion.

The whole app seems to be completely avoiding any spoilers, which is strange when apping a character like Milla. As another anon said, apps from the very start of JRPGs always have a "I don't know the canon that well" vibe.