Preheat oven to 450 degrees. Combine the peppers, eggplant, squash, onion, and mushrooms on a sheet pan, Drizzle with the olive oil and season with 1 teaspoon salt and pepper and crushed red pepper flakes. Roast until tender, about 15 minutes. Leave oven on.
Cook the penne in salted water for 8 minutes (they will cook more in the oven so undercook), drain and put in a large mixing bowl with the roasted vegetables and any pan juices. Add the sauce, herbs, fontina, mozzarella, and ¼ cup Romano or Parmesan cheese. Gently mix until fully combined. Pour into a greased 9 by 13 (or similar) baking dish. Sprinkle the remaining Romano or Parmesan over the top. Bake uncovered for 15 minutes. Serve with fresh basil leaves to garnish.