Preheat oven to 400°F. Toss the cubed butternut squash with olive oil and spread evenly on a baking sheet. Roast for 25–30 minutes, until very tender.
Meanwhile, cook the rigatoni according to the package directions until al dente. Reserve ½ cup pasta water, then drain the pasta.
Transfer the roasted butternut squash to a blender. Add the milk, Dijon mustard, garlic powder, onion powder, thyme, sage, nutmeg, salt, and black pepper. Blend until completely smooth.
Melt the butter in a large saucepan over medium heat. Whisk in the flour and cook for 1–2 minutes.
Slowly whisk the butternut squash mixture into the butter and flour mixture. Cook for 3–4 minutes, stirring frequently, until the sauce thickens.
Reduce the heat to low. Add the Gouda, cheddar, and Parmesan a handful at a time, stirring until each addition is melted and smooth.
Add the cooked pasta and stir until evenly coated. Add a splash of reserved pasta water if the sauce is too thick.
For the crispy topping, combine the panko breadcrumbs, Parmesan, and olive oil in a small bowl.
Transfer the mac and cheese to a greased baking dish. Sprinkle the breadcrumb mixture evenly over the top.
Bake at 375°F for 10–15 minutes, until the cheese is bubbling and the breadcrumb topping is golden and crisp.
Serve warm. Enjoy!
