At the end of the day, people watching this show in the future will be able to tell it was made around 2020 no matter what. Whatever Adira prefers to be referred to as is what I'm going to go with.To be perfectly honest, while I have no issue with an enby character, I do feel like it's not realistic to presume the use of "they" as the pronoun of choice would exist for 1,200 years. I mean, there's barely been consensus on it for a decade here in reality. Seems like we'd develop new pronouns - especially because we'd have experience with all kinds of alien races with more than two genders.
Saru referring to Adira as "her" isn't something I'm going to take as anything to go by, since Saru probably doesn't know Adira's non-binary and wasn't there to correct him.