I think it goes beyond biology as well, the way a cisgender woman grows up in society vs the way a transgender woman grows up is very different and can affect them greatly. There is nature and nurture differences between cisgender and transgender women that can’t be ignored but somehow it’s offensive to point out. It’s true. I believe there is a bit of a misconception about how offensive these things really are. I personally find and believe the backlash is again, due to those conversations usually only being had to invalidate the person or to force them to explain their identity.
It also upsets people because, as I mentioned in my above post, people get defensive because it’s pointing out a fact that they already know. Many trans people already know their biology is not identical to their cis counterparts as well as socially their experiences differ. It becomes a problem because those conversations are generally had, not to come to an understanding, but to discredit or discriminate against trans people, hence their defensiveness.