TO ROAST THE SQUASH:
Preheat oven to 400 degrees F.
Toss butternut squash with olive oil and garlic in a large bowl. Season with salt and black pepper. Pour out onto a foil-lined baking sheet.
Roast about 25 minutes, until lightly golden brown and tender.
Add roasted squash to food processor and puree until mostly smooth.
TO MAKE THE BREADCRUMBS:
Melt 2 Tbsp butter over MED heat in a small saucepan. Continue to cook, swirling the pan occasionally. Once the butter has turned golden brown and smells nutty, turn off the heat. Pour butter over the panko and sage in a small dish. Use a fork to toss it all together, and set aside.
TO MAKE THE MAC AND CHEESE:
Preheat oven to 375 F.
Bring a large saucepan of water to a rolling boil. Add some salt and the pasta and cook, stirring occasionally, until 3-4 minutes LESS than the package directions. Drain and transfer to a large bowl and drizzle with olive oil and stir.
Heat a medium saucepan over MED-HIGH heat and melt the butter. Add the flour and whisk, stirring well, until the flour is mixed in, and cook about 1 minute. Whisk in the milk, half-and-half, nutmeg and salt and pepper. Simmer, whisking often, smoothing out any lumps, for about 5 minutes. Remove from the heat and add two-thirds each of the Gruyère and cheddar. Stir until smooth. Add about 1 cup of the pureed butternut squash and stir to combine well.
Pour the cheese sauce into the pasta bowl and toss to combine. Add pasta to a greased 13x9 baking pan (or any pan from 2.75-3.3L capacity). Sprinkle the remaining one-third Gruyère and cheddar and all of the Parmesan. Top evenly with the panko breadcrumbs.
Bake until the top is lightly browned and the sauce is bubbly, about 15 minutes or so. Let stand for 5 minutes before serving