I agree that the story isn't well written on that part, but I don't think that the story weights on her being a trans/futa. I mean, girls can be insecure about anything, especially on a pretty big mark on their bodies. I mean, I have a cousin which has a pretty bad self-esteem because she has a mole on her chest (and she's actually pretty beautiful), I think her justifications over being insecure are pretty much valid.
Following the story after that she felt relieved when she heard that her parents died could imply anything, since they hated her for trying to emulate Grace's style till they trying to suffocate her to follow rules that she wasn't interested in the first place - and that could be anything, like military rules, religion aspects and traditions.
It's not like I liked what they did with her, because she is a fan-favorite character and wasn't implying anywhere so far that she could be a trans, but if that was the case, then probably DC shouldn't give an option for that.
But, for real, the only thing I wouldn't want for all this situation is brainless people claiming that "giving a option of choose" "decreases trains(sic) visibility".