Preheat the oven to 375 degrees F. Coat the bottom and sides of a 9-by-13-inch baking dish with cooking spray.
Add just enough pizza sauce to the baking dish to coat the bottom. Begin to layer with half the pasta (uncooked), half of the remaining sauce, half of the mozzarella, half of the Cheddar blend, a pinch of Italian seasoning and some red chile flakes and black pepper. Repeat the layers a second time.
Press the layers down to level and add 1/2 cup water to the dish along the sides (to not mess up the top). Top with the pepperoni. Sprinkle over some red chile flakes and another pinch of Italian seasoning and black pepper.
Bake until the edges are bubbling and the pepperoni is beginning to curl on the edges, 50 to 60 minutes. Remove and immediately top with the Pecorino-Romano and hand-ripped basil. Allow to cool about 10 minutes before slicing.