Preheat your oven to 400°F (200°C) and grease a 9x13-inch baking dish with butter or cooking spray.

Bring salted water to a boil in a large pot, add short pasta, and cook according to package instructions until al dente, about 8-10 minutes. Reserve about ½ cup of pasta water before draining and set aside.

Melt 3 tablespoons of salted butter in a large skillet over medium heat. Add diced onion and sauté for 3-5 minutes until translucent, then add minced garlic and cook for another 30 seconds.

Sprinkle 2 tablespoons of all-purpose flour over the onion and garlic mixture, stirring for about 1-2 minutes. Then add 2 tablespoons of tomato paste and cook until slightly deepened in color.

Add drained canned diced tomatoes and slowly whisk in 2 cups of whole milk until combined. Season with Italian seasoning, red pepper flakes, salt, and pepper. Let simmer for 5-7 minutes until thickened.

Stir in 1 cup of shredded mozzarella and ½ cup of shredded Parmesan cheese until melted. Add in the chopped cooked chicken and fold gently to coat it in the creamy sauce.

Fold the cooked pasta into the sauce, ensuring every piece is coated, then transfer to the prepared baking dish and sprinkle remaining cheese on top.

Bake uncovered for about 20 minutes, or until the cheese is melted and golden.