Cook pasta in a large pot of boiling salted water 1 to 2 minutes less than package instructions. Drain, rinse with cool water, and return to pot.
Meanwhile, heat 4 tablespoons butter in a medium saucepan over medium-high heat. Add flour; cook, whisking, 1 minute. Add milk, cayenne, nutmeg, and 2 teaspoons salt; bring to a simmer. Cook, whisking, until mixture is thick enough to coat the back of a spoon, 2 to 3 minutes. Whisk in cheeses until smooth. Pour over pasta; toss to coat. Divide among baking dishes.
Melt remaining 2 tablespoons butter; toss with breadcrumbs. Sprinkle over pasta. Cover tightly with plastic wrap; freeze up to 3 months.
Preheat oven to 375 degrees. Place frozen dishes on a baking sheet; remove plastic. Cover with foil. Bake until bubbling, 60 to 70 minutes for large dishes, 40 to 50 minutes for small. Remove foil; continue baking until golden, 5 to 10 minutes more.