Reduce oven to 375 degrees F. Cook macaroni according to package directions, drain and set aside.
In a large pot, cook macaroni according to package directions. Drain and set aside.
While macaroni is cooking, add roasted squash and ½ cup vegetable stock to a blender. Blend until smooth.
In the same large pot used to cook the macaroni, melt 2 tablespoons butter or ghee over medium-high heat. Once melted, add diced onion and shallot. Cook for about 5 to 7 minutes, until onion is translucent.
Add garlic and cook for 1 to 2 minutes. Reduce heat to medium and add in 2 tablespoons flour and 1 tablespoon dried mustard. Stir continuously for about 3 minutes, careful not to burn.
Reduce heat to low. Add in 2 cups alternative milk. Stir continuously until the consistency of gravy is reached. Season with dried sage, ½ teaspoon salt and ¼ teaspoon black pepper.
Remove from heat and stir in butternut squash puree and about ⅔ of the shredded cheese, reserving the rest.
Return cooked pasta to the pan and stir until well combined. Taste and adjust seasoning, as needed.
Pour into a 2-quart baking dish and sprinkle remaining shredded white cheddar on top. Bake for about 25 minutes, or until cheese is melted and bubbly.
Serve.