Hello there,
to the question above, no, there won't be a system to remove futa or femboy, the characters are created in a way where interaction with them is not needed, if going to the gym you can simply train by yourself, and in the case of Vanessa you can just study and leave.
In regard to this comment, this is incorrect, you don't need to do Phoenix for the harem ending, all endings were removed but the way to attain Charlotte and Anna's harem ending was by simply sharing Anna with Charlotte and kicking both Josef and Adrian.