Okay I'm getting some great responses and it makes me realize I didn't explain very well and might be wrong about the character. Let me try explaining more in depth before I change that and hearing more responses. First, I am not trying to be edgy. This came up organically when talking about the character to another person about the book. So let's start with the race:

The race all look female. It seems I misinterpreted asari, so I'll throw that analogy out. Biologically they are female, but because all of them are female, there is no 'male' gender. They are born in sets of three (not necessarily triplets, but always three when babies are born) and in each set of three which look almost identical to any outsider (kinda like how triplets look identical until you get to know them sometimes, then you see personality quirks or other things that help you differentiate them) only one of the three can breed. They can breed with others of their race as well as other races, but the babies will always look like the main race. Which is why I equated them to the asari. The asari have something similar if I remember correctly. So apologies for confusion there.

The main character, let's call him Sam for simplicity's sake, was raised outside of his culture. His mother and aunts had to flee their home country and found a new home in this new land. In this land, they appear as human females to the people. They are not, but to keep their cover they roll with it. So he doesn't know he's not supposed to identify with any gender but female because that's what everyone around him says. However, his mother falls in love with a halfelf male and he becomes a father figure, which gives him an idol in his life that is male. Due to tragedy, he and his sisters are taken from the family. He goes through a lot of hardship that ultimately drives him insane and he loses all identity of self. So this new character, let's call her Sarah, finds him and wants to restore his sanity.

Now, sarah is wanted by an enemy, not important for this discussion. She knows they are looking for a woman, so she disguises as a man and is therefore definitely not trans. She's just hiding. She uses the same idea for Sam because she rescued him and didn't want others to find him and throw him back into the predicament he'd had before. Sarah is one of his aunts, but he doesn't know this because of the memory loss. So she restores some sanity to him, but he has no memory of his former life. He knows biologically he looks female, he didn't 'discover' this. But he's in disguise as Sam, because Sarah told him that was safe.

Now, he gets separated from Sarah. He continues hiding, not know who he's running from. The reader doesn't know he's biologically female at this point because it's all in first person view. Most of what I typed up there has not been revealed at all. It's all background stuff or plot stuff that wouldn't come out. But I have a scene where Sam is with father figure, let's call him Luke, who doesn't recognize Sam as his daughter due to the scars on him and the fact that he sees a boy. He hasn't seen his daughter since she was a preteen and he doesn't realize that's who it is. He drops plot information about his daughters and wife, but Sam doesn't understand the relevance. Now, the problem I have is that the reader also wouldn't know that because they think Sam is a boy. So I wanted a flashback scene where Sarah is talking about disguising them and the reader finds out their biology. If that was where I left it, I wouldn't even have discussed this further with you guys, but here's where it continues and made me think trans and not just cross dresser.

Later in story, Sam is found out by enemies as his true identity and also starts remembering his former self. Now him being discovered isn't a shame thing, it's because someone sees through his disguise. There isn't really a big deal about it because the enemy doesn't care what gender he is, he only cares that he is Sam. I wasn't trying to imply they shamed him into that discovery, it was more like "oh, that's Samantha.That's who I've been looking for." Despite this, and despite remembering his former self, he doesn't want to go back to being Samantha. He has grown up as Sam and identifies with him. Remembering his past changes his personality some, but ultimately, Sam is who he feels he is and he doesn't want to revert back to a person he doesn't feel like any more. In my head, I always though he idolized his father figure and wanted to be like him and that even if he weren't taken away from his home he would have identified as male because of this. I did typo dysphoria, I apologize for that. The reason I think he wouldn't want to change his body is because of the physical trauma he endured (none of which is sexual) and the lack of control over his life during that time. He is okay with who he is physically and doesn't want to change that, but he feels like he is Sam. Is this not trans? I am very ignorant in the subject and am not trying to jump on a fad. Honestly, I'm only writing the story because it's a cool story (in my head, obviously biased) and I have nothing to do with my life at the moment. I may not pursue publishing it if it comes out as garbage. But when discussing Sam with another person, they asked me why he doesn't become Samantha as soon as his real identity is discovered by his enemies and I said it's because he doesn't feel like he is Samantha, even if he remembers who she is. He said that means Sam is trans because he identifies with being male despite being physically female. And honestly, the biology thing with the race can change to where they identify as female if that's the issue, it's not set in stone, this is all fiction. But looking into Sam, it doesn't feel right reverting him to that preteen state he was, even though that was the happiest time in his life.

You guys are giving me great feedback and I am really leaving out a ton of details of the story because it would be a bit much to put here. I hope this clears up some of my thought process and helps you guys give me a better viewpoint on this character. I really don't want to offend anyone and I realize I can't make everyone happy, I can at least try to be sensitive to the topic. Thanks again