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Preheat oven to 350°F. Coat a 2-quart broiler-safe baking dish with cooking spray. Bring a large pot of lightly salted water to a boil. Add penne; cook 11 minutes, or according to package directions. Drain.
Meanwhile, melt butter in a medium saucepan over medium heat. Sprinkle with flour and cook, whisking, 1 minute. Whisk in milk, onion flakes, dry mustard, salt and cayenne. Bring to a simmer over medium-high heat. Reduce heat and simmer, whisking, 3 minutes. Remove from heat.
Toss Swiss, Cheddar and Gouda together in a medium bowl. Whisk 2 1/2 cups of the cheese into the milk mixture until smooth. Stir sauce into the pasta. Spoon half into the prepared baking dish. Top with half of the remaining cheese. Repeat layering, ending with cheese.
Bake for 20 minutes. Increase heat to broil and broil for 3 to 4 minutes, until bubbly and browned.