Roast the Butternut Squash:
Preheat your oven to 400°F (200°C).
Toss the butternut squash cubes with a little olive oil, salt, and pepper. Spread them out on a baking sheet in a single layer.
Roast for 20-25 minutes, or until the squash is tender and lightly caramelized. Let it cool slightly.

Cook the Pasta:
While the squash roasts, cook the pasta according to the package directions. Drain and set aside.

Make the Butternut Squash Sauce:
In a blender or food processor, combine the roasted butternut squash, milk, cheddar cheese, Parmesan cheese, garlic powder, onion powder, and a pinch of salt and pepper. Blend until smooth and creamy.

Make the Cheese Sauce:
In a large skillet, heat the olive oil (or butter) over medium heat. Once hot, whisk in the flour to create a roux. Cook for 1-2 minutes until the mixture is slightly golden and bubbling.
Slowly pour in the butternut squash mixture, whisking constantly to avoid lumps. Bring the mixture to a gentle simmer and cook for 5-7 minutes until the sauce has thickened. If you prefer a creamier texture, you can stir in the mozzarella cheese at this point.

Combine the Pasta and Sauce:
Add the cooked pasta to the skillet and toss it to coat in the butternut squash sauce. Cook for an additional 1-2 minutes to ensure everything is evenly heated through.

Serve:
Once everything is combined, taste and adjust seasoning with additional salt and pepper if needed. Garnish with fresh parsley or thyme, if desired. Serve immediately and enjoy!