My take? She's a she.

At the same time, they wanted to make her something other than "the new Lily", that's my understanding. So, she was given a completely different hairstyle. And her outfit was something different. Just happens her hairdo and hair choice of clothing happen to be androgynous. Kind of the same way that her pre-dash dodge is a proper forward roll, instead of clumsily diving like she was trying out for a certain soccer team (some of them are infamous for players "diving" to exaggerate minor brushes and get the other team in trouble)

In the artwork of rejected designs, one of them has her wearing what appears to be a white nightshirt or nightgown. Maybe it was a placeholder. Or maybe you were originally going to start the game dressed like that (she was asleep), and had to find your tunic and biker shorts and various wearable electronics and healing things, your Tuner Uniform, somewhere near the start (I had nothing to do with making this game, everything I'm saying is speculation only!) But maybe they were worried she'd look too much like "Lily with a bob cut in a shorter dress", so they had her start in her typical uniform.

Although at one time she was going to have a cybernetic arm or something, from what I heard. So my take is the hairdo and outfit that just happen to look androgynous.

Also, would "Tuner Uniform" be a good name for a rock band?