Preheat oven to 400F.
Place squash halves on a baking sheet and drizzle them with 1 tablespoon EVOO, salt and pepper. Place them cut side down and transfer to the oven. Roast until tender, about an hour. Remove from oven and cool.
Once cool enough to handle, scoop the flesh out of the squash and transfer it to a food processor. Process until smooth.
Place a pot of water over high heat for the pasta. Once at a boil, add some salt and the pasta, and cook to al dente according to package directions. Drain the cooked pasta and return it to the pot it was cooked in.
While the pasta water is heating up, place a small skillet over medium-high heat with the butter. Once melted, add the flour and cook about a minute. Whisk in the milk and cook until the liquids come up to a bubble and the sauce thickens, 2-3 minutes. Add the squash puree, nutmeg, cinnamon and sage, and season with salt and pepper to taste.
Add the sauce to the pot with the reserved cooked pasta and toss to coat. Turn everything out into a baking dish and sprinkle the top with both cheeses. Transfer to the oven and bake until the cheese is brown and bubbly, 10-15 minutes.
Garnish casserole with the toasted almonds and serve.