[Highlight spoilered text to unspoiler]
Enki: Look at his design + how the fandom talks about him.
- In the second game, a Catholic* priest calls Enki an "effete facet" while discrediting his work. Part of Enki's backstory is that he attempted suicide via ritual sacrifice because he felt that he had reached the limits of his body.
- Part of Enki's backstory is that he was forced to fight against his twin sister to find which of them was stronger. It's ambiguous who won, but it's implied that it was his sister. This isn't really secret woman evidence but I do think it's thematically interesting with a transfem reading.
- Getting more into spoilers now: When enki has a vision of his "New God" form [that is, who Enki would become if he ascended to godhood], it tells him that he needs to kill his ego and leave behind his mortal body, and says verbatim "the only way for me to continue existing was to change." What else am I supposed to take from that.
- Also, Enki's true ending entails rejecting becoming a New God [for context, becoming a New God means continuing a corrupt system of power that's held back humanity for centuries] and instead seeking Enlightenment, a state associated with divine androgyne Nosramus.
Nosramus: Nosramus is defined by their androgyny first. One of the first lines introducing them states that "You [the player] cannot quite tell if the alchemist is a woman or a man," and then the rest of the game [and half the fanbase] exclusively he/hims them.
There are in-game books that reference Nosramus, and they have an [in-universe] "original" and "updated" version. The "original" version [which was written closer to their human lifespan] she/hers them, and paints them in a more sympathetic light than the "updated" version, which he/hims them and frames them as actively malicious. Half the fanbase takes these books as evidence that nosramus is transmasc.
Speaking of their backstory [spoilers again] Nosramus was once part of a group of five people called "The Fellowship" who were going to ascend to become New Gods. When Nosramus refused to ascend, they were cast out of the Fellowship and supernaturally forgotten by history. If you ask the New Gods about nosramus, they'll say that "He supposedly understood the true nature of the greater scheme and thus refused his ascension. He is since forgotten in our eyes and must be left in the darkness for the time he will rot."
Not to mention that like, the trope of "Otherwordly/Magical and Androgynous" that Nosramus embodies is typically a transmisogynized role [see: the inspiration that Fear & Hunger takes from Soulsborne games]