Heat oven to 350°. Coat a 3-quart broiler-safe baking dish with nonstick cooking spray.
Bring a large pot of lightly salted water to boiling. Cook pasta 8 minutes in boiling water; drain.
Meanwhile, in medium-size saucepan, cook bacon over medium heat, until crisp, approximately 6 minutes. Transfer to paper towels.
Carefully pour off drippings, leaving 2 tablespoons in 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 cup 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° for 20 minutes.
Increase oven temperature to broil and broil 3 minutes, until top is lightly browned. Cool slightly before serving.
Garnish with green onions, if desired.