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You had me in the first half. She was there, but she didn't force you to listen to her story. She just existed. Like, sure, she was clocky; that's just how it is for girls who transition later in life. She mentions that she's been on a journey, and if you, the player, choose the appropriate dialogue option, she'll tell you her story, which, oddly enough, might be the less realistic thing. There are a lot of trans people who would prefer not to share that, because there are a lot of not-trans people who will change their tune and use information about a person who no longer exists to hurt the person they've transitioned into.

Zagreus (and Melinoë presumably) on the other hand are not obviously pan until you, the player, start pursuing same-sex relationships. Given that Hades and II are based on Greek mythology, it might come as no surprise, but it's not like there's an aspect of facial or body shape that obviously identifies someone as being lesbian/gay/bi/pan like there tend to be for trans people (especially femmes and women, ESPECIALLY in a world without cosmetic surgery, hand-wavey magic aside). She didn't hurt you, so be happy that some people did feel seen and move on with your life.