Cook macaroni according to package directions; drain. Set aside.
Meanwhile, preheat oven to 350 degrees F. For cheese sauce, in a medium saucepan cook onion in hot butter until tender. Stir in flour and black pepper. Add milk all at once. Cook and stir over medium heat until slightly thickened and bubbly. Add cheeses, stirring until melted. Stir in cooked macaroni and chili beans in gravy. Transfer mixture to an ungreased 2-quart casserole. Top with corn chips.
Bake, uncovered, for 25 to 30 minutes or until bubbly. Let stand for 10 minutes before serving. Garnish with jalapeno peppers and/or green onions.