As a non-binary user, I have some thoughts about this:
1) I am actually very happy with the existing setup - I don't recall anyone in-game using any pronoun at all to refer to my commander, and that's very comfortable. And it's been that way since 1984.
2) More flexibility in Holo-Me appearances would be good, but (a) that goes way beyond questions of gender and (b) it's a lot more coding work, so I'm not going to stress about it.
3) Some of you who say "I don't care about your gender identity, but stop rubbing it in my face" are telling on yourselves. We're not required to be invisible; 'live and let live' entails letting us live in the same shared spaces as the rest of you.
4) Singular 'they' is well-established in English, and pretending otherwise is prescriptive nonsense. No-one is pretending to be a monarch or a nation or whatever. Get over it.
5) As far as I can recall, the game doesn't gender the generated NPCs either. The only place I recall seeing gendered pronouns is in Galnet articles. And in those, diverse sexual orientation is already well-represented (Jupiter Rochester's separation from his husband, for example); it would be nice to see non-binary representation as well, but only as and when it can be introduced casually; the last thing I'd want is a big fanfare.
6) ETA: My partner has suggested the possibility of free simple pride flag decals, which I think could work.