1. Cook the Macaroni: Bring a large pot of salted water to a rolling boil. Add the elbow macaroni and cook according to package directions until al dente. Drain the pasta well and set aside. Do not rinse the pasta, as the starch helps the sauce adhere.

2. Prepare the Roux: In a large saucepan or Dutch oven, melt the 3 tablespoons of unsalted butter over medium heat. Once melted, sprinkle in the 1/4 cup all-purpose flour. Whisk continuously for 1-2 minutes until a smooth paste forms and it smells slightly nutty. This is your roux, the base for your creamy sauce.

3. Whisk in the Milk and Seasonings: Gradually pour in the 3 cups of milk, whisking constantly to prevent lumps. Continue to whisk until the mixture thickens and comes to a gentle simmer, about 5-7 minutes. Stir in the salt, black pepper, and ground nutmeg. The sauce should be thick enough to coat the back of a spoon.

4. Incorporate Butternut Squash and Cheese: Remove the saucepan from the heat. Stir in the 1 1/2 cups of cooked butternut squash puree until fully combined and smooth. Add the 2 cups shredded sharp cheddar cheese, 1 cup shredded Gruyere cheese, and 1/2 cup grated Parmesan cheese, stirring until all the cheese is completely melted and the sauce is smooth and creamy.

5. Combine Pasta and Sauce: Add the drained cooked macaroni to the cheese sauce. Stir gently until all the pasta is evenly coated with the rich, orange-hued sauce.

6. Bake (Optional, for a crispy top): If desired, transfer the macaroni and cheese to a 9×13-inch baking dish. In a small bowl, combine 1/2 cup panko breadcrumbs with 2 tablespoons melted butter, then sprinkle evenly over the top of the mac and cheese. Bake in a preheated oven at 375 F (190 C) for 15-20 minutes, or until bubbly and the topping is golden brown. If you prefer a stovetop version, simply serve immediately.