Preheat your oven to 400°F. Line a baking sheet with aluminum foil, if desired, for easy clean up.
Lay the butternut squash face-up on the baking sheet along with the garlic and shallot. Drizzle the olive oil all over the veggies, and sprinkle them liberally with the seasonings.
Roast in the oven for 45 minutes-1 hour, until the squash is soft enough to pierce with a fork. Note: if you use pre-cut butternut squash cubes, reduce the cooking time to about 40 minutes.
Remove from the oven and allow to cool slightly.
Meanwhile, cook the pasta according to package instructions. Reserve 1/4 c of pasta water before draining.
Scoop the insides of the butternut squash into a blender along with the softened garlic cloves and peeled shallot. Add the reserved pasta water and blend into a smooth consistency.
Pour the butternut squash pasta sauce into a pan and let it come to a simmer over medium-low heat. Mix in the grated gouda cheese until smooth.
Add the pasta to the sauce and toss until all of the pasta is coated in the sauce. Serve warm, topped with grated parmesan cheese and brown butter sage.