Heat oven to 350 degrees F. Coat a 3-quart broiler-safe baking dish with nonstick cooking spray. Bring a large pot of lightly salted water to boiling.
Cook cavatappi 8 minutes in boiling water, then drain. Meanwhile, in medium-size saucepan, cook bacon over medium heat until crisp, 6 minutes. Transfer to paper towels. Carefully pour off drippings, returning 2 tablespoons to pan. Add butter.
Whisk in flour until smooth. In a thin stream, whisk in milk. Stir in onion flakes, salt and pepper. Bring to a boil over medium-high heat, then reduce heat and simmer 2 minutes. In large bowl, toss together cheddar, colby-Jack and mozzarella.
Remove milk mixture from heat; whisk in American cheese and 1-1/4 cups of the cheddar mixture. Toss bacon pieces with remaining shredded cheese.
In pasta pot, combine cooked pasta and cheese sauce. Pour half into prepared dish. Sprinkle with a generous cup of the bacon-cheese mixture. Repeat layering.
Bake at 350 degrees F for 20 minutes. Increase oven temperature to broil and broil 3 minutes, until top is lightly browned. Cool slightly before serving.