If you never see her penis, or interact with it, and know that by the time you get into any sexual situations that involve her nether regions she'll be female again, why does it really matter?
Alright, I know to some people it does matter, but to most it doesn't and the extra work load to avoid those situations, while keeping the story making sense for both sets of players (those who disable futa content and those who don't) isn't really worth it to be honest. It'd be a huge amount of work developing two coinciding stories that would take away from developing other parts of the game to satisfy a small portion of the player base.
If it really bothers you, maybe this isn't the game for you and that's fine
Not every game is suitable to every persons tastes. As much as I would like to offer options that allow everyone to play how they want, it's just not a feasible task for one person without seriously slowing down development.