Preheat Oven and Cook Pasta:
Preheat oven to 375°F (190°C). Bring a large pot of generously salted water to a boil. Add pasta and cook until 2 minutes shy of al dente, keeping it slightly firm. Drain and set aside.
Prepare Walnut-Sage Topping:
In a large sauté pan over medium heat, melt the butter. Add walnuts and 1 tablespoon of chopped sage, cooking for about 5 minutes until walnuts are toasted and fragrant. Season with a pinch of salt and transfer to a bowl.
Make the Sauce:
Return the pan to medium heat. Add olive oil, mushrooms, and onion. Sauté until softened, about 8 minutes. Add tomato paste, garlic, and red pepper flakes, cooking for 3-4 minutes until tomato paste darkens and caramelizes. Gradually stir in spinach, cooking until wilted. Add oregano, salt, pepper, nutmeg, and the remaining 2 teaspoons of sage.
Add Liquids and Cheese:
Pour in vegetable broth, stirring to release any browned bits from the pan. Add pumpkin purée, Parmesan, and ½ cup of fontina cheese, stirring until the cheese melts and the sauce becomes smooth. Add cooked pasta and stir until noodles are well-coated with the sauce.
Assemble and Bake:
Transfer the pasta mixture to a greased 13×9-inch baking dish. Sprinkle remaining fontina cheese over the top, followed by the walnut-sage mixture. Cover with foil and bake for 15 minutes at 375°F. Uncover and bake for an additional 10 minutes, or until the cheese is melted and golden.