Preheat the oven to 425°F (220°C) and line a baking sheet with parchment paper.
Peel, seed, and cut the butternut squash into 1-inch cubes. Place them on the lined baking sheet, drizzle with olive oil (about 1 tbsp), and lightly season with salt and pepper.
Wrap the halved shallots and peeled garlic cloves in foil with a drizzle of olive oil and a pinch of salt. Place them on the baking sheet. Roast everything for 30-40 minutes until the squash is caramelized and tender.
Cook pasta according to the package instructions, then drain and rinse under water (to avoid sticking). Reserve ½ cup of pasta water just in-case you need to thin the sauce more. Place the pasta back in the pot and set aside.
In a blender, combine the roasted squash, shallots, garlic, 1 tsp salt, ½ tsp pepper, thyme, parmesan or nutritional yeast (start with 2 tbsp), vegetable broth, coconut milk, Dijon mustard, and balsamic vinegar. Blend until creamy.
Pour sauce over pasta in the pot, stir, and adjust thickness with reserved pasta water or extra vegetable broth. Heat over medium for 2-3 minutes until it is warm.
(Optional) Fried Sage Leaves: Heat 1 tbsp olive oil in a small sauté pan over medium heat. Add fresh sage leaves and let them get crispy for about 30 seconds to 1 minute. Transfer to a paper towel to rest. You can also do this with freshly chopped sage.
(Optional) Pan-Fried Pancetta: Add chopped pancetta to a large saute pan over low-medium heat and “fry” for about 3 - 5 minutes until the fat is rendered and it is crispy.
Serve the pasta immediately in individual bowls, topped with fried sage, extra black pepper, and optional pancetta. Enjoy!