Those are birth defects though. For instance, we still understand humans as being bipedal despite anomalies that prevent a tiny fraction of humans from being bipedal.
`XXY` is a valid combination of sex chromosomes. The person has two `X` chromosomes so is female. The person also has one `Y` chromosome so is male. Which sex is the person? Is it a birth defect?
XXY is Klinefelter syndrome. By definition it's a condition where boys and men are born with an extra X chromosome. Their sex is male because, also by definition, the presence of a Y chromosome means male.