Yeah, stuffed crust is definitely patented by Pizza Hut. You need legal permission from Pizza Hut to make it (or at least in the US). On top of that, it's impossible for Domino's to effectively make a stuffed crust pizza with their current dough making methods.
What pizza chains do Stuffed Crust?
In 1995, Pizza Hut changed the pizza-eating game forever with our Original Stuffed Crust® Pizza. Warm and melty cheese is stuffed into the crust of our traditional pizza dough, then topped with our classic marinara, 100% real cheese made from whole milk mozzarella and your favorite toppings.