Willa looks like my Figara.
I miss my Figgy. 
How is that? The “orange” gene is sex-linked, to the X chromosome. If the mother has at least one orange gene, then a tortoiseshell female can result even after a mating with a black (i.e., non-orange) male. Unless I have misunderstood the origin of the orange patches…
Could be a chimera. There’s at least one notorious (in the cat show/breeding world, at least) case of a purebred Maine Coon who is a.) calico colored, and b.) very proudly, and prolifically, a virile male.
Up at the farm the folks were having a problem with feral cats eating all the birds and squirrels. So Dad started a system of live trapping and shooting them. These were not “nice” cats either but mean tomcats. Over the years he killed dozens. The birds began to come back.
Now normally he would check the traps and the cat caught would be mean and hissing and angry until one day the cat he noticed was female and seemed friendly and docile. He just let that cat go. Next day the cat was back in the trap and he let it go again. Soon that cat would not run away but stayed around him. A while later they decided to let the cart come into the house and sort of adopted it. She became their new cat and was a good pet. She would go outside alot and rarely used a litter box. She would just scratch on the door and want outside then let them know when she wanted back in. Sometimes she would be gone a couple of days.
Later she had one kitten. She died later and the kitten is their cat.
Dad still caught and killed any other ferals.
I was assuming the mother had no orange showing; because if she did, then orange showing up in two female kittens wouldn’t have said anything about the father at all, and the vet. presumably wouldn’t comment on seeing the orange that they must have had the same father.