In FSA it's not,no one sees Ganondorf II as a kingThis is how I see it too. There is one more thing, though: IIRC in OoT, it was said that the one male Gerudo that is born every 100 years has to become king of the Gerudo. BotW on the other hand, shows that they have their own Royal family, although in this case it's only queens and princesses. Male Hylians that marry into the Royal family are still not allowed inside the city so they are not considered to be kings.
It's unexplained if the old rule that made Ganondorf the King of the Gerudo would still be in effect if a new male Gerudo is born.