So what?? Why do chromosomes matter at all? Gender ≠ sex. Anyone is allowed to identify however they want, and it literally hurts nobody.
However, trans people do actually have brain structures that mismatch their assigned sex at birth. Also, most differences of sex are just caused by hormones, so HRT really does meaningfully change someone's sex.
You should also know that human biology is not so clean cut. Intersex people exist, and for example there are people born female with a Y chromosome.