Hi, thanks for the response! I'm sorry I wasn't very clear with how I phrased things.
The subtext I gathered from the line "despite your origin, your mother made sure you would appear more feminine when your father first laid his eyes on you." was that mother had the baby's genitals surgically altered, which is comparing sex reassignment surgery to genital mutilation. And because of this, the audience is supposed to feel bad for the character because they were forced into being a woman. And because we are supposed to feel bad, it implies that it is bad.
When you kept mentioning that the character was in a more privileged position being female, it really feels like you are purposely drawing attention to it as as a key detail in how the character feels, which implied they feel the opposite.
If you wanted to draw a comparison on how women and men were treated differently why make the transition forced against their will, or have a transition at all? You could more directly compare their experiences and upbringing to their father's childhood to strengthen the tension between them and explain how the church views gender roles.
I hope this helps! Thank you for listening and not directly writing me off!