Fill a large pot with lightly salted water. Over high heat, bring to a rolling boil; stir in the macaroni and return to boil. Cook pasta uncovered, stirring occasionally, until pasta is cooked through but still slightly firm, about 7 to 8 minutes. Drain well.
In a large saucepan over medium heat, melt butter. When butter starts to foam and bubble, stir in flour; cook, still on medium heat, until flour just begins to turn pale yellow, about 3 to 4 minutes. Add chipotle, thyme, cayenne pepper, and white pepper; cook and stir another minute, then whisk in 1 cup (250 mL) of milk until smooth. Pour in remaining milk and whisk again. Bring sauce to a simmer.
Stir in Worcestershire sauce and salt; simmer on medium-low heat until thickened, about 8 minutes, whisking often. Turn heat off, then add 2 ¼ cups (625 mL) of cheese; stir until melted and combined. Add spicy Dijon mustard.
Transfer macaroni to a casserole dish; pour in cheese sauce and stir to thoroughly combine sauce with pasta. In a small bowl, mix panko bread crumbs and melted butter; sprinkle on top of macaroni and cheese. Sprinkle remaining ¾ cup (175 mL) of cheese on top.
Bake at 400°F (205°C) until bread crumbs and cheese topping are golden brown, about 15 to 20 minutes. Makes 6 servings.