The latter. I assume the confusion comes from the pronouns? I kept them the way they are because, especially at the time, it was easier to do so (me being a potato of a programmer), with the idea being that the character doesn't want to mess up. So he just keeps all his thoughts on "Sam is a guy, Sam is a guy, Sam is a guy." to not accidentally slip up.

In retrospect I think it feels that it muddied it a bit too much, as it's a question I've been getting fairly often and I assume it stems from the pronoun use after it. So, changing it to variable pronouns depending on what the MC knows has been on the to-do list for a little bit. Which should hopefully help make it clear that Sam very much sees herself as a woman and that there is no dysphoria involved.