Just went back and read Luffy and Yamato's interactions ( vol.98 on-wards in Japanese).
Luffy meets Yamato, Yamato says she is Oden, Luffy says you are a woman, Yamato says she wants to be Oden and he was a man, Luffy calls her Yama (man/guy/bro) for the rest of Onigashima, starts calling her Yamato after the battle.
Seems it is just Luffy's pattern of calling people he does not respect/care about some random name until they earn his trust. After that he calls them whatever they like to be called; Like Ivankov being Iva-Chan.
Yamato is a woman, she knows she is a woman, a woman who is also the man Oden. Yes the double think is real. Funny enough if Yamato did get pregnant she would still call herself the father and on the birthing bed say something like "Is now when I go to boil the water?"