Although I don’t see anything wrong with this, I think @Boundegar is referring to the feline instinct to bury their excrement, not to litter boxes per se, which is why once most kittens are shown where the box is, they don’t really need to be trained to use it.
On the other hand, dogs have an instinct to mark their territory, but we train them not to (at lest indoors). Moreover, domesticated cats and dogs aren’t themselves natural. Ancient humans bred them to be quite different from their ancestors.
I do think there is a valid question to be asked whether imposing certain behaviors on even domesticated animals is ethical. For example, dipshits who lock large dogs in small apartments 24/7 and only take them out to do their business two or three times a day without giving them any real exercise. But, for my part, I don’t think training cats to use the toilet is cruel. Of course (and I apologize if this sounds smug) we don’t have that problem since our two cats are working animals with a cat door and access to the garden where they get their fill of rodents and help fertilize the soil. Disgusting? No more than chemically processed cow dung, IMHO.