Oda actually took effort to make Kiku appear trans. He made her effeminate, both in appearance and dressing. He made other characters treat her as a woman.
In contrast, he did nothing of the sort for Yamato. He made her another oversexualised Nami clone. He shows off her tiddies at any opportunity.
He had Luffy react with disbelief when Yamato introduced themselves as "Kaido's son". He had Ace's crew call her Kaido's daughter.
Had Oda been intending to depict Yamato as male, he could have them actually place effort in modifying their appearance to appear less feminine.
They could use breast bindings instead of wearing clothing that shows off their tiddies. Oda could have introduced them as Kaido's son instead of his daughter.
Oda could have had Yamato correct Ace's crew for addressing them as Kaido's son if that was indeed misgendering them.
He made her effeminate, both in appearance and dressing.
He made other characters treat her as a woman.