My understanding is that the X chromosome carries the gene for red cat fur. Female calicos have one X with the red fur gene and one without. If a cat only has X chromosomes that carry the red fur gene, they'll be an red-furred cat, which is why the only male calicos are XXY. An XY male cat with the red fur gene on their X chromosome just comes out red.
I don't see how some separate "simple congenital deformity" other than an extra X could account for red fur.
I could be wrong, I'm not a cat scientist, I just grew up knowing hundreds of cats.
That said, if somebody gave me the option to bet on a calico cat being female, I would always take that bet because I'd only be wrong about one in three thousand times (0.03333...% of the time) if the cat was randomly selected, whereas other coat colors it'd be 50-50.
