Preheat oven to 400° Fahrenheit.
On a large baking sheet, toss together the cubed butternut squash, peeled garlic cloves from one whole head of garlic, peeled and cut shallots, fresh thyme leaves, olive oil, salt, and red pepper flakes. Bake for 30 minutes, or until butternut squash is very soft.
Remove baking sheet from oven and let cool slightly. While the squash cools, bring a large pot of water to a boil. Once boiling, add in a big pinch of salt and the pasta. Cook pasta according to package instructions.
Once butternut squash is slightly cool, add to a blender along with the vegetable broth, raw cashews, and sage. Blend until completely smooth.
Right before draining the pasta, reserve 1 cup of pasta water. Then, drain the pasta and return to the pot along with the butternut squash sauce. Add ¼ cup of pasta water at a time to the pasta to thin out the sauce, as needed.
Serve immediately with additional fresh herbs.