Heat 1 tablespoon olive oil in a large ovenproof skillet over medium heat until hot; add mushrooms and saute until they begin to brown, 3 to 5 minutes. Remove and set aside. In same skillet, heat 1 tablespoon olive oil over medium heat, add Italian sausage and onion, and cook about 3 minutes, breaking up sausage into bite-sized pieces. Add butternut squash and cook, stirring occasionally, until sausage is browned and squash begins to soften and deepen in color, about 10 minutes. Add garlic, sage, salt, pepper, cinnamon and crushed red pepper, and cook, stirring, 1-2 minutes. Add tomatoes, 2-1/2 cups water and mafalda pasta; bring to boil, cover skillet, reduce heat and simmer until pasta and squash are tender, 15 to 18 minutes.
When pasta and squash are tender, uncover skillet, add reserved mushrooms, and, if needed, continue to cook a minute or two to evaporate excess moisture (do not cook until totally dry). Combine shredded cheeses in a small bowl and stir about half the cheeses into the skillet, mixing well. Sprinkle remaining shredded cheeses on top and, if desired, place in a 400º oven until cheese is melted and lightly browned, 5 to 10 minutes (see NOTE). Garnish with additional fresh sage leaves if desires and serve with whipped ricotta to dollop on each serving.