Season the butternut squash with 1 tbsp olive oil, 1/2 tsp salt, and 1/4 tsp pepper Roast on a baking sheet, flesh side down, at 425 for 30- 45 minutes until tender. Let cool, scoop flesh out of skin into a bowl, set aside.
Bring large pot of water to boil. Season with a small handful of salt, boil pasta for 8-10 minutes. Drain and transfer to a large baking dish.
Add 1 tbsp olive oil to a small skillet. On medium high heat, saute onion and 1 tsp of salt for 8 minutes.
Add garlic and seasonings. Saute for 1 more minute, then add 1/2 cup of broth. Turn off heat.
In a blender, add the parmesan, butternut squash, sauteed veggies, and the half and half. Blend until it forms a smooth and creamy puree. Thin out with broth, water, or half and half as needed. It should be thick and creamy but also pourable like a cheese sauce.
Add sauce to pasta and mix well. Top with gruyere and fontina. Bake at 350 for 30 minutes.