Preheat oven to 400 degrees Fahrenheit. Generously grease a 9 x 12 baking dish with butter and set to the side.
In a large 4-quart Dutch oven or heavy bottom pot, heat 2 tablespoons olive oil over medium heat. Add the shallots and cook until translucent, about 3 to 5 minutes. Add the garlic and stir for one minute until fragrant. Add the butternut squash cubes followed by the stock and bring to a quick boil followed by simmering. Add the herbs and red pepper flakes, if using, and simmer until squash is tender, about 7 to 10 minutes.
While the squash simmers, bring a separate pot of salted water to boil. Add in the dried pasta like macaroni noodles or elbow macaroni and cook until just al dente, about 6 minutes.
Once the squash is tender, remove from heat and, using an immersion blender (or a standalone blender), blend mixture until smooth. If the mixture feels a bit too thick, add in ¼ cup of stock at a time until consistency is smooth.
Add in the créme fraîche, nutmeg, and grated cheese. Stir to allow the cheese to begin to melt into the sauce.
Pour sauce over the pasta and stir to combine. Pour into the prepared baking dish. Sprinkle remaining cheese and breadcrumbs over the top.
Bake for 30-40 minutes until edges are golden and cheese is bubbly and melty. Garnish with fresh herbs and serve.