Place butternut squash, cut-side down, on a baking sheet.
Roast squash in the preheated oven until soft, 40 to 50 minutes. Remove squash flesh from skin and set aside. Reduce oven temperature to 375 degrees F (190 degrees C).
Bring a large pot of lightly salted water to a boil; cook the rotini at a boil until tender yet firm to the bite, about 8 minutes; drain.
Melt butter in a large saucepan over medium heat. Whisk flour and mustard into melted butter until smooth, about 1 minute. Gradually whisk milk into flour mixture until the mixture has the texture of heavy cream, 5 to 7 minutes. Remove from heat.
Stir butternut squash, white Cheddar cheese, and Cheddar cheese into milk mixture until cheese is melted. Stir rotini into cheese mixture. Pour cheese mixture into a 9x13-inch baking dish. Top with bread crumbs.
Bake in the preheated oven until bread crumbs are golden, about 10 minutes.
Nutrition Facts Per Serving: 414 calories; 15.6 g fat; 51.9 g carbohydrates; 17.7 g protein; 46 mg cholesterol; 307 mg sodium. Full nutrition.