Well for one thing, the X chromosome is essentially the common base genetic material that all humans, male and female, share. This is why I always disagree with the whole argument that AMAB can not transition to female because, AFAIK, most, if not all, secondary sex characteristics are determined by hormones. Because this is true, the Y chromosome mostly effects the body through hormone production that essentially trigger other Y chromosome genes in the body. By modifying the hormones, you are shutting down those triggers and the resulting human form is, in my opinion, completely female.
Also, many believe that hormone levels in early development can have an impact upon the brain, which is one current theory as to why we are the way we are.
I also believe that this can be spiritual as well where one may be a feminine spirit. I think of myself as being feminine spiritually and physically in mind and body but happen to be AMAB.