Heat a medium-large pot over medium-high heat. Once hot, add the tablespoon of olive oil. Add the onions and sauté until translucent and just starting to brown, approximately 7-9 minutes. Add the garlic and sauté for 1-2 minutes until fragrant. Place onion and garlic mixture in a small bowl and set aside.
Add the butternut squash and vegetable broth to the same pot and bring the mixture to a boil. Reduce the heat to a simmer. Simmer for 20-25 minutes or until butternut squash is fork tender. Remove from heat, reserve ½ cup of the vegetable broth. Drain the butternut squash and let cool to room temperature.
Meanwhile, as the butternut squash is cooking, prepare the pasta. Bring another large pot of water to a boil. Cook the pasta according to the package instructions to al dente. Drain and set aside.
Preheat the oven to 350°F. Grease a 9x13 baking dish and set aside.
Once the butternut squash has cooled, add it to a high-speed blender or food processor. Add the onion/garlic mixture, the ½ cup reserved vegetable broth, milk, Dijon mustard, Worcestershire sauce, nutmeg, thyme, and black pepper. Blend until smooth and creamy, adding additional milk or broth if too thick. Taste and adjust seasoning to your liking.
Place the pureed butternut squash sauce back in the pot you boiled it in. Turn the heat to medium-low to warm. Add 1 ¾ cups of cheese and stir until it has completely melted.
To a large mixing bowl (or the large pot you boiled the pasta in) add the pasta and sauce and stir well. Pour the pasta into the prepared baking dish and spread evenly.
In a small bowl, combine the breadcrumbs, olive oil, and paprika. Sprinkle evenly over the mac and cheese. Bake in the oven for 10 minutes. After ten minutes sprinkle the remaining ¼ cup shredded cheese over the top and place back in the oven until the cheese is completely melted on top. Enjoy!