Grease a 13" x 9" baking dish with 1 tbsp olive-oil.
Place the butternut squash in a large sauce pot of hot water and bring to a simmer. Simmer for approximately 15 minutes or until the squash is tender when pierced with a fork. Drain and reserve.
Bring a large stock pot of salted water to a boil. Add the pasta and cook based on the package instructions to al dente.
In a large stock pot, heat 4 tsbp olive-oil over medium heat. Add the shallot and sauté for about 2 minutes, until the shallot just begins to turn golden. Add the flour and whisk to blend thoroughly for about one minute, stirring constantly.
Slowly pour the milk into the flour roux, whisking constantly. Add the cream and continue whisking until thickened.
Take 1 cup of the sauce mixture from the pot and add it to a blender or food processor with the butternut squash. Process until smooth. Add the butternut squash mixture back into the pot with the rest of the sauce mixture and whisk to combine. Set aside 1 cup of Gruyère cheese, and add all of the remaining cheese to the sauce. Stir to melt and combine. Taste for seasoning and adjust with salt and pepper if desired.
Add the truffle oil and the pasta. Mix well and pour into the prepared baking dish. Top with the reserved cheese, and bake for 25 minutes until the top is golden brown and the pasta bubbly.