Heat oven to 350°F. Butter or oil an 8-inch baking dish. You can use non stick spray as well.
Cook the penne 2 minutes less than package directions, since it will finish cooking in the oven. Rinse the pasta in cold water, and set aside for later.
Melt the butter in a heavy- bottomed saucepan, or Dutch oven, over medium heat, and whisk in the flour. Continue whisking and cooking for 2 minutes and the mixture will be clumpy and start to turn golden brown.
Slowly add the milk, whisking constantly to create a thick sauce. Cook until sauce thickens, about 8 minutes, stirring frequently. Remove from heat.
Add 1¾ cups of the Beecher’s Flagship cheese, ¼ cup Just Jack cheese, salt, 1/8 teaspoon chili powder, and garlic powder. Stir until the cheese is melted and all ingredients are incorporated, about 3 minutes.
Combine cooked pasta and sauce in a medium bowl, and mix carefully but thoroughly. Scrape pasta into the prepared baking dish. Sprinkle the top with remaining cheeses and then the remaining chili powder.
Bake uncovered for 20 minutes to let the cheese bubble on top. When done cooking, let it rest for 5 minutes before serving.