Veery few trans women have even partially transitioned, let alone fully.
But the few who have still biologically have different chromosomes, different skeletons, different endocrine systems, different immune systems, different internal reproductive systems, don't and never have had periods, don't and never have had the possibility of pregnancy, different metabolisms, on average taller and stronger, not just because of their size but relative to a biological female of similar size...
Oh, I'm sorry, did you think a female human is just like a male human except with tits and a fuck-hole? Something you can assemble from parts? No. We are complete, entire beings in our own right.
But that's just a side track, because your question about biology misses the point.
We don't segregate men and women in vulnerable situations, or create female-only protections and opportunities to empower women, simply because we are biologically different. We do this because living with that biology in this society has consequences. The difference between a man - an adult human male - and a woman - an adult human female - is not simply their bodies today, but the whole lives lived, in those bodies, with the capabilities they bring, the experiences they do and do not have, the way others see and treat them and what that in turn leads them to believe about themselves, their place in society and their relationships with their own and the opposite sex. We do it because too often, male bodied people are socialised to believe they are better than women, more real than women, more important than women, and therefore entitled to women's bodies, focus and support. And too often, women are socialised to believe it too.
So even if you could throw a bio-switch and transform a male body into one that was 100% female, you'd still have a person without that experience of being born a female child and growing into a female adult, a person whose life experience up to that point was that of a male.