See, I don't see a problem with this. Remove male/female flags for clothing, perhaps add in a pitch shifter to adjust the pitch of the existing voices up or down, maybe (if you REALLY want to cover all bases) change from four body types to a height-weight-muscle slider system and you've got a HECK of a lot more flexibility in character creation. It certainly isn't the same as a character selection system in which you can choose your gender identity from a huge list but it'd give people more flexibility than the binary options.
Choosing your gender identity from a huge list sounds very daunting - the idea of having pitch sliders and body sliders for this actually sounds like the more welcoming of the two options: start with bio-male or bio-female frames and work from there. But this is getting wildly off-topic.
I think my Agent would probably form a close platonic, if not romantic, relationship with a (male-identified) AI. I'd imagine the two could have quite a few things in common, given what happened in the Agent storyline.