No way Arthur Morgan would support something so delusional as trans men being "anyone who is a man inside". Like be so for real. He knew a crazy person was a crazy person in the game.
1- Arthur doesn't treat Sadie like a crazy woman because she "dresses and acts like a man", and back then, that would be as "weird as being trans"
2- Arthur doesn't judge any effeminate guy for being that way, he just doesn't care.
3- He calls Margaret, Margaret, even if it's a guy dressed for a show, he gives him the requested pronoun.
4- Arthur is against all these prejudices stablished by "rich people" and "civilization"
5- Arthur (and Dutch) think people should be free
6- Even if he didn't understand, if it's someone who's being judged by "society norms", Arthur is supporting. Like he does with racism (even if he doesn't understand it well at the start of the game), with feminism (even if he doesn't understand why voting is important)
7- Roger Clark supports Trans people
8- Arthur would support queer people overall. He doesn't judge Chatenoy for cross dressing, he also doesn't judge Margaret, ge also doesn't judge Bill for being gay, doesn't judge Sadie for wearing "men clothes".
9- Arthur doesn't think women who wanna fight and do 'men things' are crazy.
10- Arthur doesn't treat queer characters as crazy because they're queer.
11- Even if Arthur thought cross dressing or wanting to be a different gender was something odd, weird or different, he would respect those people, because to him respect it VERY important and he IS a marginalized person
12- In old times in many places, a man being abused sexually would "be less man" or "not be a man anymore" or "not be an actual man", and Arthur was abused, at least 1 time in canon and 2 times subtext but veeery close to canon (his father and O'Driscolls gang rape in Bleased are the Peacemakers). So well, I doubt Arthur thinks he's "less of a man" because of that. Meaning....he doesn't follow 1899 society prejudice and misconceptions.
13- Trans people aren't crazy, no reason for Arthur to think they're crazy. Unusual? Different? Sure. Crazy? I doubt.
14- Many women in the game do "men" things, Arthur isn't against that, and he also doesn't think they're crazy. Arthur is practical and supports freedom. If a guy wants to wear a skirt, whatever. I see Arthur more indifferent than thinking trans people are crazy.
Also, he's more arguments I doubt you gonna even bother reading:
He consistently judges people by their actions—not where they come from, how they look, or what others say about them.
Arthur is a man who’s learned to look deeper than surfaces.
He has a fundamental belief in equality and freedom because of Dutch and Hosea.
Arthur in a pretty consistent way demonstrates a commitment to protecting individual freedom and standing against societal discrimination. He's friendly with black and native American people during a highly racist historical period, and he even participates in women's suffrage protests. That's a broader pattern of supporting marginalized groups against oppressive systems . His core ideal revolves around living life as one sees fit without judgment or restriction from "civilized society," which would naturally extend to accepting trans men for who they are.
Honestly I think upon learning someone is trans, he would rather respond with warmth, protection, and a focus on their inner character rather than their gender identity. Happines is more important than social norms to him.
Arthue could make stupid jokes here and there due to his environment, but he would not hold malicious intent . His fundamental character—a man who protects the vulnerable and questions societal prejudice—suggests he would learn, accept, and fiercely defend his trans friends. He even complains many times as story goes (to Dutch) that the gang used to help people in the past and now they were using people. His first bank robbery was about giving money to poor marginalized people. Trans people are marginalized people, back in 1899 and even today.
In summary, Arthur Morgan's character arc, actions, and moral compass as detailed in the search results all point toward him being an ally who would judge a trans man based on his character, courage, and heart, ultimately affirming his identity and right to live freely and happily.