Preheat oven to 350˚F. Cook penne 2 minutes less than package directions. Rinse in cold water and set aside.
Melt butter in a heavy bottomed saucepan over medium heat. Whisk in flour. Continue whisking and cook for 2 minutes. Slowly add milk while whisking. Cook until sauce thickens, about 10 minutes, stirring frequently. Remove from heat.
Add 1-3/4 cups Flagship cheese, 1/4 cup Just Jack cheese, salt, 1/4 tsp. chili powder, and garlic powder. Stir until cheese is melted and all in¬gredients are incorporated, about 3 minutes.
Combine pasta and sauce in a large bowl and mix carefully. Scrape into an 8-inch baking dish. Sprinkle with remaining cheese and chili powder.
Bake, uncovered, for 20 minutes. Let Mac & Cheese sit for 5 minutes before serving.