"I'm a guy, please refer to me as such."
Being trans is self-identifying as a gender other than the one you were assigned at birth…which is exactly what Yamato does. It's okay for people to stop identifying as such, of course (happens in real life all the time). Yamato as a character written by a nominally out-of-touch millionaire cishet author with poor understanding of gender (in general) or trans issues in a magazine published for children by a massive, multi-million dollar publishing company is extremely important because he is invariably giving some trans boy the representation he's likely never going to receive from his family or friends, let alone society, growing up. Oda's dragging his feet and lack of clarity is a major issue and we should be critical of him and Shueisha for their handling of these subjects in their massively popular work. To borrow a tired quote, "With great power comes great responsibility."
Oda's handling of Kiku is extremely problematic and shows a pretty lousy understanding of being transgender, so it really wouldn't surprise me if Oda doesn't know that transgender men exist, too. With Yamato being an admirer of Oden...trans people do this all the time? Plenty of us name ourselves after characters or people who played a big role in our understanding of who we are.
Oda wants to touch upon important subjects and political messages with his art and that's fine and dandy but it also requires him to have a degree of actual experience with, knowledge and understanding of these things. He's a millionaire, would it kill him to hire a few consultants? Or hell, check out these communities himself? Or just...not mystery box worthless shit and actually just outright explain his ideas beforehand through text? If Oda's intention was not for Yamato to be trans perhaps he should actually, I don't know, have the responsibility to make a clear statement beforehand? His platform is a very important one and he and the publisher should be aware of this without dropping all this weirdly vague bullshit like breadcrumbs on the way to a massive shit sandwich years down the line.
And I'll agree with you, I don't think Oda's qualified to touch this subject with the longest of poles. Handling this subject matter tactfully is difficult in general. But in terms of the authors intent I don't think it's anymore than "Lol Kaido's kid is calling themself by the name of Kaido's worst enemy" not a character embracing what they feel to be their true gender identity. It's more like, Yamato identifies as Oden who just happened to be male than Yamato identifies as a male and is named Oden. If Oden had been female it'd be the same to Yamato.