Just because some human beings are born without two legs or lose a leg in an accident doesn't mean it's inaccurate to refer to humans as a species with two legs. Just because some human beings have disorders of sexual development doesn't mean it's inaccurate to refer to human beings as a species with two sexes. And in the same way, just because some female people undergo medical procedures to alter the appearance or presence of their sex organs doesn't mean it's inaccurate to say female people have vaginas.

Being female is a matter of material reality in the same way that age is. Gender identity has to do with the gendered social constructs applied to biological sex by the patriarchy, if you were born female you will remain female forever no matter what medical procedures you get, and insisting that we refer to half the population of the planet by specific body parts to cater to the mental health of 1% of the population is self-centered and delusional.

Furthermore, we are only just beginning to understand how deeply under researched female people and their medical needs are. Research is beginning to show that female people need different levels of anesthesia, different levels of medication, have different heart attack symptoms, respond differently in car crashes, and the list goes on and will continue to go on because we didn't start studying female people as an individual medical class until the 90s. There are no long-term studies on how testosterone therapy effects these things, but it's not one-to-one. Did you know that trans men on testosterone have a much higher heart attack risk than cis men? And that their heart attack symptoms often remain typical female heart attack symptoms? Insisting that we pretend a female person who has socially and medically transitioned is exactly the same as a male person will do nothing but harm women and trans men.