Preheat oven to 375°F.

Bring a medium pot of salted water to a boil over high. Add pasta, and cook according to package directions for al dente. Add butternut squash during the last 3 minutes of cooking. Drain and set aside.

While pasta water comes to a boil, heat oil in a large Dutch oven over medium-high. Add sausage; using a wooden spoon, break up sausage into medium-size clumps. Cook, undisturbed, until bottom side is lightly browned, about 6 minutes. Stir sausage; cook, stirring and breaking up sausage into smaller pieces using a wooden spoon, until cooked through, about 3 minutes. Add spinach, stirring to wilt completely. Transfer sausage mixture to a medium bowl. Do not wipe Dutch oven clean.

Melt butter in Dutch oven over medium. Add garlic, thyme, pepper, nutmeg, and ½ teaspoon salt; cook, stirring often, until fragrant and thyme leaves pop, about 1 minute.

Sprinkle flour over garlic mixture; cook, whisking constantly, until mixture thickens and is light tan, about 2 minutes.

Gradually add milk, whisking constantly. Bring to a gentle simmer over medium, whisking bottom of Dutch oven often. Reduce heat to low; cook, stirring often, until mixture is thickened enough to coat the back of a spoon, about 5 minutes.

Remove Dutch oven from heat. Gradually whisk in Fontina and Parmesan cheese, 1 cup at a time, until melted and smooth, about 1 minute. Whisk in remaining 1 teaspoon salt.

Stir in cooked rigatoni, sausage mixture, and butternut squash. Transfer to a 13- x 9-inch baking dish lightly greased with butter; spread in an even layer. Sprinkle evenly with blue cheese and pinenuts. Place baking dish on a baking sheet.

Bake, uncovered, until bubbling around edges and top is browned in spots, 40 to 45 minutes. Let cool 10 minutes before serving.