Cook pasta per package directions; reserve ½ cup pasta cooking water.
Meanwhile, heat oil in large skillet on medium. Add onion and ¼ teaspoon each salt and pepper; cook, covered, stirring occasionally, until tender, 8 to 10 minutes. Stir in garlic and cook 1 minute. Sprinkle with flour and cook, stirring, 1 minute. Carefully add butternut squash and ½ teaspoon salt and cook, stirring occasionally, until slightly thickened, 5 to 7 minutes.
Whisk in milk and bring to a simmer. Whisk in cream cheese, cayenne, and nutmeg. Add 6 ounces Cheddar and Gruyère and stir until melted and smooth. Remove from heat and toss in pasta, adding 1 tablespoon pasta water at a time to loosen sauce to desired consistency. Serve sprinkled with toasted panko and chopped parsley.
