Perhaps I'm somehow selecting the wrong thing, but when we are introduced to Riven, the story seems to flag my character as trans, even when I selected the "I am happy with my body without surgery or hormones" option. Perhaps that is a trans flagging option? If so, maybe making that a little more clear for players would be a nice addition. If it's not, then I think this is a bug. Or is the MC just locked to being trans no matter player input?
The option it seems you wanna pick is "You smiled, seeing your body. You were confident and happy with how it looked." I tested it out and that one, as well as one at the bottom about being neutral towards your body both don't give you the line about being trans, and I assume this is the case with the one that explicitly mentions being cis as well though I didn't bother testing.
So basically, it seems to be, if the option mentions hormones and/or surgery your character will be trans if not they'll be cis.