It stems from lanugaue, culture and social conditioning. The penis itself doesn't dictate a patrichal attitude, any more than a stomach does.
Disclaimer: in the following I will distinguish between penis and vulva because I’m commenting on the relationship between these typically sexed organs and cultural constructions like patriarchy. I’m not taking them to be the definition of male,man,woman or female, and I’m not saying they aren’t that either. My point is entirely tangential to how one defines male/man/female/woman: it’s that saying something is purely cultural is not an argument to say it is irrelevant or has no material impact.
And when all the penis-havers (and vulva havers ) have grown up in a language, culture and society that is free from patriarchal conditioning, where there are no statistically measurable differences between the penis-people’s violence, opportunities and financial outcomes and the vulva-people’s, when no one looks at a penis-person and a vulva-person and thinks, “oooh, we’d better employ the penis-person because the vulva person will probably want maternity leave”, when no one says to the little vulva-person “oh you’re such a good person, helping your sibling” and to the little penis-person “oh, you’re such a clever person building your models”, when the penis-person is just as likely to be a full time parent and suffer career loss as the vulva-person, THEN it will be safe to say all women, trans or not, can be treated identically (apart from sport, and medicine, and some sort of provision for career impact of breast feeding, and other purely biological differences).
But until that happens, people with a penis have a hugely different experience of womanhood than people with vulvas, and it does huge to disservice to those of us with vulvas to have the opportunities, rights and protections that were created to protect women (vulva havers) in a patriarchal society opened up to penis-havers who may indeed be Women by a deeper definition but have had a totally unrelated experience to the one that Women’s rights were designed for.
Because Women’s rights are not a matter of identity, or abstract definition, or validation. They are a practical response to the practical impact of having a child-bearing physiology (or appearing to have one at birth) and being defined as and raised as a woman within patriarchy. Transwomen don’t need them, and they do those of us that do a grave disservice by demanding them.