I'm not going to ... further derail the thread to converse about Motoko, but it's hinted at, that she's not really really female, or that being female in body is a choice for her and that it does not match her gender. The second GIG Memory library episode was not an actual place but a strange unexplained anomaly. She actually disappears physically, and ends up in a virtual world temporarily, though where her physical body was is not explained.
It's more her gender that's never solidified, it's heavily hinted at that she was a little girl at one time, but never full canon confirmed.