Preheat oven to 400 degrees F.
Spray a 2 quart baking dish with cooking spray, set aside.
Cook pasta until al dente, set aside.
Bring a large pot of water to a boil. Add in butternut squash and let it boil until tender, about 8-10 minutes.
Drain, then divide the squash in half into two bowls and set one aside. Take the other bowl and mash squash.
In a small bowl add 1 cup of milk, flour, mustard, rosemary, white pepper, and salt, stir together and set aside.
In the same large pot that you boiled water in, add butter and place over medium-high heat. Add shallot, and cook, until it starts to brown, about 1 to 3 minutes, stir frequently to avoid burning.
Slowly add 2 cups milk and bring to a boil, whisk in flour until smooth and starts to thicken. Add in the remaining milk/flour mixture and whisk until well combined and thick, remove from heat and add in shredded Gruyere cheese, stir until completely melted.
Stir in the mashed squash. Then slowly stir in the macaroni and the remaining chucks of squash. Transfer to the prepared dish.
Top with breadcrumbs, sprinkle with paprika, spray the top of the bread crumbs with cooking spray so that can turn easily turn a golden brown.
Place in the oven and bake until bubbling hot and browned on top, 10 to 15 minutes.
Remove from oven and cool at least 10 minutes before serving. Serve and enjoy!