@Nah bro Yong Yong is officially MTF trans
I don't remember how it was shown in the manga
But in the novel, when Yong Yong first transformed into a human - she chose female body and iirc was referring to herself as female (if not then ig femboy?)
MC was 100% sure at that point, that Yong Yong is a guy. Presumably he was quite familiar with Yong Yong's internals as a dragon, as he was monitoring a lot of things on the egg and hatchling
So he tried to check if Yong Yong has a member (by sacrificing his clone), but failed and just went "as a father, I have to be supportive"