Cook pasta according to package directions; drain.
While pasta cooks, melt butter in a large skillet over medium heat; add onion, and sauté 5 minutes or until golden brown. Whisk in flour until smooth. Cook, whisking constantly, 2 to 3 minutes or until flour is light brown. Gradually whisk in milk; bring to a boil, whisking constantly. Reduce heat to low. Stir in provolone cheese until melted. Stir in peppers, nutmeg, and salt and pepper to taste.
Remove from heat, and stir in cooked pasta. Spoon mixture into a 13- x 9-inch baking dish coated with cooking spray. Sprinkle evenly with Parmigiano cheese.
Bake at 350° for 20 minutes or until golden and bubbly.