Nah, you can keep spaces just for women while remaining ideologically consistent.
Woman is a protected class, and protected classes are exclusive by nature. A person can choose to waive the protections granted to them, ad hoc or modify the circumstances of their protected status. As an example, a person with a disability might choose to reject accommodations in a specific circumstance, or might pursue medical treatments that change or void their need to receive accommodations. It's a reasonable comparison to say that FtM require protections for their trans status, but not for their female status since they have revoked those protections.
It's not really important whether you can actually change sex, it's about the fundamental purpose of protected spaces.