Preheat the oven to 400°F (200°C). In a baking dish, toss the cubed butternut squash, chopped shallots, and garlic cloves with ¼ cup olive oil, salt, and pepper. Roast in the oven for 30-40 minutes until the squash is tender.
While the squash is roasting, cook the shell pasta according to package instructions until al dente. Drain and set aside.
Once the squash is roasted, transfer the squash, shallots and garlic to a blender or food processor. Add 2.5 teaspoons balsamic vinegar, 1 teaspoon onion powder, ¼ teaspoon nutmeg, and 1½ cups milk. Blend until smooth and creamy.
In a large bowl, mix the blended butternut squash with 2½ cups grated cheddar cheese, 2½ cups grated Gruyere cheese, and ½ cup finely grated pecorino or Parmesan cheese. Stir until well combined.
In a large pot, combine the cooked shell pasta with the cheese and squash mixture. Stir until the pasta is evenly coated.
In a small bowl, mix ¾ cup panko breadcrumbs with 1½ teaspoons extra-virgin olive oil until the breadcrumbs are evenly coated.
Transfer the mac and cheese mixture to a greased baking dish. Sprinkle the panko breadcrumb mixture evenly on top.
Bake in the preheated oven for about 20-25 minutes, or until the top is golden brown and crispy.
Let it cool for a few minutes before serving. Enjoy your Butternut Squash Mac and Cheese!