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.