Well gender is determined by both genotype and phenotype. I never heard of people who’s gender phenotypes don’t match their genotypes, but in those situations, I guess the phenotype outweighs the genotype.
So, since medical transition does in fact change the phenotype, you accept that some amount of transition makes people a different gender.
No because it doesn’t change the complete phenotype. The Skeloton doesn’t change and the testicles are mutilated but don’t become full functioning penises and vaginas. Trans women can’t give childbirth. I’ll change my views if they invent the technology for men and women to trade brains for bodies.
Uterus transplants are already possible, so 'Trans women can't give childbirth(sic)' is on a ticking clock (plus, plenty of cis women can't either...). Skeletal structure can change with early enough access to hormones, and again I don't think you're going to be x-raying a woman on the street and telling her she has to be a man now because her hips are too narrow
For any phenotypical difference between men and women, then either some cis people would be classified as the wrong gender or it is or soon will be modifiable with medical transition. Usually both.