Option to set "special characters" sex is not always working, few times i try to set "classroom admirer" and "harraser" to choose trans-female and they swap around back for male/female...
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IIRC, release notes say the game will override your selected NPC sexes to make ones you're "supposed to be" attracted to based on you're character's sexuality. I don't know what your setup was, but I heard if you want them to be trans-female you have to be attracted to women and hope it doesn't RNG them cis-female. I haven't actually looked at the code to confirm if that's how it does it though.