Preheat the oven to 425°F (218°C). On a baking sheet, toss the cubed butternut squash, halved shallot, and smashed garlic cloves with olive oil, oregano, chili flakes, salt, and pepper. Roast for 20–25 minutes until tender.Remove garlic from their skins. In a food processor or blender, purée the roasted squash, shallot, garlic, and ricotta until smooth. Season with salt and pepper to taste.In a large oven-safe skillet with high sides, bring 3½ cups of water to a boil. Add rigatoni and cook, stirring often, until just al dente, about 8 minutes. Do not drain the water.Stir the butternut squash purée into the skillet along with the milk or cream, Italian seasoning, spinach, and chopped sun-dried tomatoes. Stir until fully combined.Add the shredded gouda and grated parmesan cheese, mixing until melted and creamy.Remove from heat. Top evenly with shredded fontina or provolone cheese.Bake uncovered for 15–20 minutes, until bubbly and golden brown on top.Garnish with extra oregano or fresh basil if desired and serve hot.