Preheat oven to 350° F. Bring 1 gallon of water and 1 ½ tsp. salt to a boil in a Dutch oven; add pasta. Cook 8-9 minutes or until al dente. Drain; rinse with cold water. Toss with 1 Tbsp. oil.
Melt butter in a large saucepan over medium high heat. Add onion, and sauté 4-5 minutes or until tender. Add flour, and cook, whisking constantly, 1-2 minutes or until smooth. (Do not brown or flour). Add half-and-half, next 2 ingredients, and remaining 1 ½ tsp. sea salt, and bring to a simmer. Cook, whisking constantly, 5-6 minutes or until thickened. Gradually add cheeses, stirring until blended. Transfer mixture to a large bowl; stir in cooked pasta. Spoon into a lightly greased 13x9 inch baking dish. Sauté chipotle pepper in remaining 2 tbsp. hot corn oil in a small skillet over medium heat 30 seconds or until mixture begins to smoke. Remove from heat, and quickly stir in bacon and panko until coated. Sprinkle mixture over pasta. Bake at 350° F for 15-20 minutes or until golden and crisp on top. Serve immediately.
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