Preheat oven to 375 degrees. Spray a 13x9 pan with nonstick cooking spray. Set aside. Prepare the macaroni al dente according to directions on package. Drain and set aside.
In a large skillet over medium-high heat, cook red onion and red and green peppers, about 3-4 minutes. Add the Italian sausage and cook until no longer pink, breaking up with a wooden spoon, about 4 minutes. Add garlic and continue to cook one more minute. Remove from heat and set aside.
Melt 6 Tbsp. butter over medium heat in a large dutch oven. Whisk in flour and cook for one minute. Slowly whisk in milk, cream, Italian seasoning, salt and pepper. Stirring constantly, continue to cook for 6 minutes until nice and thick. Add the marinara sauce, 3 1/2 cups fontina cheese and 2 cups mozzarella cheeses and mix until the cheese is melted and the sauce is smooth. Add the cooled pasta, the Italian sausage and veggies and the pepperoni slices.
Pour into the prepared dish and sprinkle with the remaining 1/2 cup fontina and grated parmesan cheeses. Bake until bubbly and nice and golden browned, about 30 minutes. Sprinkle with fresh chopped basil, if desired. Serve immediately.