Cook 8 ounces elbow macaroni in salted boiling water as the label directs for al dente. Reserve 1 cup cooking water, then drain.
Melt 4 tablespoons butter in a large saucepan over medium heat. Add 1/4 cup flour and cook, whisking, until smooth, 2 minutes. Whisk in 2 cups whole milk and 1 teaspoon kosher salt. Bring to a simmer and cook until thickened, 5 minutes. Stir in 6 ounces each shredded Colby Jack and cheddar until smooth, then add the pasta, thinning with the reserved cooking water as needed. (The sauce will thicken as it bakes.)
Transfer to a 3-quart baking dish. Prepare your topping; sprinkle over the mac and cheese. Bake at 400 degrees F until golden, 15 to 20 minutes.