Preheat the oven to 400 degrees F. Place a sheet of aluminum foil on a large rimmed baking sheet. Cut the top and bottom off of the butternut squash, then stand the squash upright on a cutting board. Cut in half from the top down, then scoop out the seeds. Brush with the olive oil and place cut side down on the prepared baking sheet. Roast for 30-40 minutes or until very tender.

Remove from heat and allow to cool. When cool enough to handle, scoop out the butternut squash flesh with a large spoon and place in a high powered blender or food processor. You will have roughly 1 1/2 cups of butternut squash. Add 1/2 cup of the milk and process until smooth. At this point you may store the butternut squash puree in the refrigerator for up to a few days until you're ready to make the mac and cheese.

Grease an 8×8" baking dish with butter or cooking spray and set aside. Preheat the oven to 350 degrees.

Cook the pasta until very al dente, about 2 minutes less than the package instructions specify as it will continue to cook in the oven. Drain well.

While the pasta cooks, heat 1 tablespoon of butter in a medium sauce pan over medium heat. Add the shallot and cook 2-3 minutes or until softened, then add the garlic and smoked paprika and cook 30 seconds longer.

Add 2 tablespoons more of the butter to the sauce pan and allow it to melt. Once melted, sprinkle in the flour and whisk constantly until it's golden brown and bubbly and smells like shortbread, about 1 minute. Remove the pot from heat and add about 1/3 of the milk in a slow steady stream while whisking constantly until the mixture resembles a smooth paste. Whisk in the remaining milk until smooth, and place back over medium heat. Whisking constantly, bring the mixture to a boil, then reduce the heat and simmer until thickened and boiling, about 3-5 minutes longer. The sauce should be thick enough to coat the back of a wooden spoon.

Remove from heat and whisk in the butternut squash puree, 1 1/2 cup of the cheese and the thyme. Taste and add salt and pepper as needed, then add the pasta and stir until well coated. Place the pasta mixture the prepared baking dish and spread evenly. Top with the remaining 1/2 cup of cheese.

Melt the remaining 1 tablespoon of butter in a small bowl, then add the breadcrumbs and toss until well coated. Sprinkle the breadcrumb mixture over the casserole and bake until bubbly and golden brown, about 20-30 minutes. If the top browns too quickly, cover with greased foil to prevent sticking. Serve and enjoy!