Hii! This is a bit of a complex question o---o
In both books, the gender of the main character has no bearing on playthroughs. The Archon is always referred to as "they" and only by a neutral title, and the answer to the gender at the beginning of the game only matters for that single scene exclusively (with the special consideration that it is about the birth of the archon and throughout the story it is implied that their gender, and any fact of self-identification is fluid).
In part, the inclusion of gender could have made the scenes feel more personal and immersive, but on the other hand, it also cuts down on the character and gameplay of the romance in this open, fluid form. The Secunda is androgynous, genderfluid and queer by default, and we try to leave out details in the story that could not be interpreted otherwise later. Still, any of your original character can be of any gender or presentation, this is an artistic interpretation for personal use and desire of everyone, all together and separately<з