Preheat oven to 400ºF.
Toss butternut squash, onion, and garlic in olive oil. Sprinkle with 1 Tbsp thyme. Lightly sprinkle with salt and pepper. Roast in the oven for 30-40 minutes, until soft and browned. Once removed from the oven, reduce heat to 350ºF.
In the meantime, cook pasta according to package directions.
When the butternut squash is done, place in a blender with your broth of choice, milk, yogurt, and nutmeg, and blend until smooth.
In a large bowl, combine pasta with squash puree. Mix in your cheese of choice (reserving 1/4 cup for topping), and 2 Tbsp fresh, chopped thyme, if desired. Salt and pepper to taste.
Spray casserole dish lightly with cooking spray. Spoon noodle mixture into the dish and lightly sprinkle with remaining cheese and parmesan cheese.
Cover with aluminum foil and bake for 20 minutes. Uncover and continue to bake for 20-30 minutes, until bubbling and lightly browned.