Bake on a rimmed baking sheet in preheated oven until bubbly and golden, 30 minutes. Remove from oven; increase oven temperature to broil. Sprinkle with reserved shredded cheeses; broil 6 inches from heat until cheeses are melted and golden, about 2 minutes. Remove from oven; cool slightly on a wire rack, about 15 minutes.
Make it ahead: Prepare through Step 2 up to 1 day in advance; cover and refrigerate. Bring to room temperature before proceeding with Step 3.
Roasted Broccoli Macaroni and Cheese: Preheat oven to 450°F. Toss together 6 cups broccoli florets (24 oz.), 1 tsp. minced garlic, 1 Tbsp. extra-virgin olive oil, 1 tsp. kosher salt, and 1/2 tsp. black pepper in a large bowl. Spread mixture in 1 layer on a rimmed baking sheet; bake in preheated oven until lightly browned, 20 minutes. Prepare recipe as directed, stirring broccoli into cheese sauce with pasta and diced cheeses before baking.
Herbed Breadcrumb-Topped Macaroni and Cheese: Prepare as directed using entire amount of cheeses through Step 2. Stir together 1/2 cup panko (Japanese-style breadcrumbs), 2 Tbsp. melted salted butter, 1 tsp. chopped fresh sage, and 1/2 tsp. each chopped fresh thyme and rosemary; sprinkle over casserole before baking. Bake until topping is golden brown. Omit broiling.