Oda DID make Yamato's gender more confusing than just a straight trans narrative.
Bon Kurei is both. Called Okama and hermaphrodite, readily accepted as being something inbetween.. but referred to in text as "he", and never really argues about it. Bon is a man that likes being pretty like a woman, and with his fruit can readily switch. Both with a male default.
Ivanokov switches fluently between either mode, so you just sort of call it as you see it at the time. Defaults to a more masculine mode, and that's what we first saw, but goes either way. I see some readers default to calling Ivankov She, and that's completely legit.
The… characters... Sanji put up with over the timeskip are an awful joke and bad taste on Oda's parts. Given that they were portayed with heavy stubble and lusting after Sanji it was kind of a crude icky area to go after and probably a failing on Oda's part. I think we're supposed to go with drag queens in those cases, men that dress in women's clothes, possbily gay, but they were a really awkward joke.
Those are all old old examples though. Oda seems to have comme a ways in the last decade on transgender issues, in particular in Wano.
Kiku wants to be a woman, is called a woman, looks like a woman, no one has any issues with calling Kiku a woman. It took a while to even figure out that she was trans.
Izo is a little trickier, he seems to be a man that dresses in a feminine way, but is only a crossdresser, and not trans. A much better example than the people Sanji dealt with.
Yamato on the other hand, IS trickier. He is drawn looing like a typical Oda girl, showing off sideboob and bare feminine arms, and is introduced by the omniscient narrator box as "daughter". (When Oda could have very easily made a more masculine flatter chested design and introduced as "son".) So, at that level, it's tricky, and easy to understand why anyone would call Yamato "she".
And yet Yamato declared he is Oden, and wants to be called a man because Oden, (which then leads to the layer of "does he want to be a man because Oden was a man and thats all there is to it? Or does he want to be a man... like Oden?) and this most recent chapter seems upset at being called Kaidou's daughter, and Luffy accepted it immediately. Whatever factors or nuances are in play, whatever Wano's cultural values bring into it (and this goes all the way back to Zoro and Kuina) Yamato wants to be called he.
Yamato explicitly wants to be called a man, so unless that changes, we should respect that. Yamato is a he, visual appearances to the contrary.
However, if that's rough for a given reader to grasp, and they refer to Yamato as she, because its a fictional character on the page being drawn in a very feminine way, and we know who is being talked about, it's okay to some degree if someone calls Yamato a she. AS LONG AS THEY AREN'T DOING IT OUT OF MALICE.
As long as they're not obviously being antagonistic or petty or vitriolic or bigoted about it, contradictory to be contradictory. Its sometimes a hard concept to grasp, even if you are open minded about it or have know trans people for years. If you haven't been exposed to that much... it's an unusual thing you just haven't had exposure to.
So please, at current, no one gets to harass other readers for using he or she. Both are still sort of correct, as as long as someone isn't being an ass about it, don't be an ass about correcting them, and try not to get offended over it.
If its a very personal issue to you and your entire life, its very easy to get wrapped in, but don't immediately assume malice... for some this is the first time they've had to deal with calling someone something other than what they look at, while you may have had years internalizing the idea.
Oda's telling something different here, he's doing a Rose of Versailles thing. Yamato is on a journey, and I imagine at the end of it he won't want to be "Oden" anymore, but will he still want to be a man?
Personally? I hedged the first couple chapters, but Yamato has specifically asked to be called he, it was made a major point immediately, and Luffy is accepting it, so I say go with "he" unless the story shifts its a different direction. (Adn that Oda did the reveal immediately instead of holding it for a dozen chapters despite the disguise is telling.)
If Oda is consistent and long term about Yamato being a man, everyone will get on the same page eventually, however it goes.
That whole "try to be understanding and both sides are sort of right" bit out of the way... If someone IS being a malicious ass about it, hit the little exclamation mark in the bottom of their post and report it rather than getting into a fight with them over it..
Also, for the record, my best friend in the entire world for 22 years is trans, and is super into gender issues, so I've been exposed to and seen a ton of non-binary stuff. So anyone who suggests for even a second I have any problems with trans people is incredibly wrong, but I also understand that in this particular case at this particular time it might be confusing or weird to some, so it's not an issue we need to get into fights over when education is better.
It hasn't been a huge deal the first several months of Yamato's existence, I'd hate for it to start being one now.