(Prefacing this by saying that I'm trans myself) I think unfortunately the situation is a little more complicated just because the character is still so new and it's hard to tell if Oda is truly treating them as a trans character or just a "a girl who think she's a man as a goof." With Oda's previous track record of handling trans characters it's hard for me personally to believe it's the former. However yeah, right now Yamato has done nothing but use masculine pronouns and say he's a man/Oden, so seeing people try and deny that can be frustrating.
Well you're actually trans, so I'll ultimately defer to you, but the way I see it, it's pretty straightforward. We have a character that explicitly describes himself as a man, as Kaido's son. Luffy (who imo is basically Oda speaking through him), the Beast Pirates, and Kaido have been 100% consistent with respecting his gender identity. Whether it's an explicitly masculine nickname, masculine pronouns, describing him/himself as Kaido's son, or the Beast Pirates calling him "young master (a term only used for young men), the text has made it clear how Oda wants us to view him. Even in Ch. 999, it's strongly implied Yamato took issue with the Spade Pirates calling him Kaido's "daughter". Like people try to latch onto to the introduction box (an admittedly very clumsy way to clarify Yamato's biological gender), but then weirdly ignore that not once has the actual characters familiar with Yamato refer to him as a woman. The only thing viewed as a gag is the Oden aspect of it (Ulti and Momo's reactions come to mind) But even Ulti still recognizes him as Kaido's son.
When the character was just introduced, existing for like 3 or so chapters at the time, I understood wanting more clarification. But now the character has been around for awhile now, and nothing has changed in regards to how they refer to Yamato. So to ignore that IMHO is to ignore basic reality. And I know not everyone is malicious about it (especially those that can at least acknowledge Kiku's gender identity), but it's very frustrating to point all this out, only for it to be ignored. Feels like the only reason people struggle with Yamato as opposed to Kiku is because he doesn't look masculine enough.
As for the counterargument of anticipating this character arc where Yamato fully grows out of the "Oden" persona, and thus goes back to viewing himself as a woman, I don't get that one either.
Like… I don't understand why people think it makes sense to misgender a character based on what they think will happen. The most common sense thing to do here is to only begin referring to Yamato using feminine pronouns once the character has actually started to view themselves as a woman. And not a moment before. You lose out on literally nothing by acknowledging how Oda currently views the character.
Even then, it's not this guaranteed thing that will happen. Yamato has since kind of chilled out with the constant talk of them being Oden, referring to himself as Yamato whenever he feels like it. And even before that, Luffy took issue with Yamato calling himself Oden, but still proceeded to give him a clearly masculine nickname. So it's certainly possible for Yamato to drop the Oden shtick, but still feel more comfortable as a man.
This is basically how I feel too, except I think you're a little more positive than I am haha. There's no doubt in my mind that there will be at least one joke with Sanji and I'm hoping it ends at just that. But like I mentioned earlier, depending on how Oda takes things, I worry that it'll be reoccurring.
The only reason I have anything close to optimism is because there is a noticeable effort on Oda's part in regards to Kiku and Yamato, like them not having caricatured designs for one thing. Now, that doesn't mean there won't be any Sanji gags, and it's not like Oda's handled them 100% perfectly. But they are still clear improvements, and I hope that that means that Oda would have the self awareness to not make it this reoccurring thing. Would be really odd to be 100% consistent so far, including with the main character of the series, and then just throw all that out repeatedly when it comes to Sanji. I can begrudgingly live with a shock value gag where Sanji's initially surprised, but if it becomes a repeat thing for either character I'd be deeply disappointed.
There's not much in Sanji's past that shows this. Lol The exceptions are his sister, children, Kiku, and old women like Shinobu. If you're a young, attractive character that has a typical female anatomy, it's over. It's one of the reasons why I don't see Yamato joining. He would break Sanji's shtick.
I mean honestly, I don't really mind the idea of Sanji being attracted to him, whether he struggles with it or not. There's nothing really wrong with that.
Really, the only things to avoid (to make me personally comfortable), assuming Yamato continues to view himself as a man, is:
1. His shtick of defending women (the bad optics of him doing that for Yamato is obvious)
2. His inability to hurt women (If Yamato steals from the Sunny's fridge, he should get his ass beat lol)
3. Maliciously disregarding Yamato's gender identity
For #3, I don't actually feel like Sanji would do this to a non caricatured trans character, even more so if Yamato actually joins the crew, but you never know I suppose. Overall, the first two things is certainly a lot to ask for from an author that very much enjoys his low hanging fruit/running gags, but I would love to be surprised…