Preheat the oven to 400 F and line a large baking sheet with parchment paper. Slice the butternut squash in half, lengthwise, and spoon out the seeds. Add 1 tbsp avocado oil to the flesh and season with salt and pepper. Place flesh side down on the baking sheet and bake in the preheated oven for 35-40 minutes or until tender. Allow to cool.
Scoop out the flesh from the butternut squash and add it to a food processor with 3 tbsp of chicken broth. Blend until fully pureed and smooth. Set aside.
Using a medium pot, heat 1 tbsp of avocado oil over medium-low heat. Add the garlic and shallot and sauté until the garlic is fragrant.
Pour the chicken broth into the pot and bring to a boil. Add the pasta and cook for 5-6 minutes, stirring well often to cook the pasta evenly. The pasta should be tender and the broth should be absorbed. Reduce the heat to low.
Add the butternut squash to the pot along with the dried sage, thyme leaves, vinegar, and extra salt and pepper to taste. Stir well.
Turn off the heat and add the shredded cheese (or nutritional yeast) and stir well.
Serve topped with fresh thyme!