Heat oven to 350°F Spray 9x13 dish with nonstick spray.
Cook penne pasta according to box and desired tenderness.
Meanwhile, in a large saucepan, melt butter over medium heat. Stir in flour, salt, and pepper. Cook until bubbly, stirring constantly. Gradually add half and half, stirring constantly. Cook until mixture boils and thickens, stirring frequently. Remove from heat. Stir in cheeses, until melted. Cheese will be stringy. Stir in milk.
Drain pasta and return to pot. Add to cheese sauce to pasta, stirring gently to coat. Pour into dish. Sprinkle with green onions.
Bake for 20-25 minutes or until edges are bubbly and mixture is thoroughly heated.