on of the things that i have to argue the most with mutations is how they interact with clothing. Mostly that when you craft something like a duster its not built for your form. What i would say is that any player made clothing made after the mutation. like if a character had a huge mutation and that character made a shirt it would fit them. so i would say mutations cause problems with found clothing but not crafted. same for armor. examples i make a iron helmet and i have horns. the helmet would be made in two locking parts a faceplate and back with hole cut out for he horns and since it come from the side the horns would not cause any problems. and yes i also mean survivor gear.
This is generally handled by having similar but separate versions of the items, which accommodate mutated anatomy. Like XL survivor mask for instance. This is because we cannot set different mutation handling in different instances of the same item.
i was more thinking of making modified versions like the horn holed helmet. or for birds a plauge doctor style gas mask with the beak being hollow for the beak of the bird mutation