To a large pot, cover cubed butternut squash (fresh or frozen) with 1 1/2 cup water. Simmer over medium heat, until squash is tender about 10-20 minutes. (If using frozen squash, it will be tender at about 10 minutes, if fresh, it will be tender closer to 20 minutes. Do not overcook). Turn off the heat and transfer tender squash to a blender.
To a blender, add butternut squash, sage, thyme, vegetable broth, salt and pepper. Puree until smooth and creamy. Set aside. Meanwhile, cook Modern Table® Elbows according to package directions.
Melt ghee in the skillet. Add garlic, and cook, stirring frequently, until fragrant, about 2-3 minutes. Whisk in tapioca starch until lightly browned, about 1 minute. Gradually whisk in almond milk, butternut squash puree and Dijon mustard. Bring to a boil; reduce heat and simmer, stirring occasionally, until reduced and slightly thickened, about 3-4 minutes.
Add the cooked Modern Table® Elbows, cheddar, and Parmesan. Stir until the pasta is evenly combined and the cheeses are melted. Top with additional Parmesan if desired.