On clothing and mutations: A JSON tag already exists allowing clothing to be worn over mutations, and you can see the XL variants of the different survivor armor pieces showcasing this. As far as realism is concerned, yes you could make clothing/armor of any shape and size, but you are essentially following a pattern in most cases so deviating substantially from that might end up causing issues, which is represented by the lower stats of the XL survivor armor. If you want more armor and clothing that fits over mutations it’s just a matter of adding the right tag to a copied version, then making a recipe for it. This would be quite easy for an amateur to do their first PR on if you’re interested in getting into contributing, although a minor discussion might be needed on what armor and clothing could or couldn’t be made mutation friendly. I can’t think of anything offhand except for power armor and hazmat suits.
On more mutations: More mutation trees isn’t a bad thing, but it means making new mutations and mutagens, which can be a whole lot of work. That said, something like a horse or snake might be an issue considering how close it is to existing mutation lines (cow and lizard/raptor) and the amount of overlap it might cause. It might be more useful to actually look at adding sub-mutation branches to the existing mutation trees, or just making existing mutation trees less specific (e.g mammal instead of cow/horse, reptile instead of snake/lizard) and allowing them to specialize once a threshold is reached or just being entirely nonspecific and allowing mutations from all kinds of animals within that category.
Super mutations: Super mutations would basically just be post-threshold mutations, which already exist and are pretty cool. What you describe sounds more like a fantasy version of existing mutation trees, which would probably be better off in a mod rather than the base game, since no real fantasy mutation trees exist thus far (with the possible exception of slime, which really just ties into the Goo, and Elf-A, which you could argue is an offshoot of the Alpha mutation).