Fill a large pot with lightly salted water and bring to a rolling boil over high heat. Once the water is boiling, stir in the macaroni, and return to a boil. Cook the pasta uncovered, stirring occasionally, until the pasta is cooked through but still slightly firm, about 8 minutes. Drain well.
Melt 1/4 cup butter in a large saucepan over medium heat. When the butter starts to foam and bubble, stir in the flour; cook on medium heat until flour just begins to turn pale yellow, 3 to 4 minutes. Add thyme, cayenne pepper, and white pepper; cook and stir another minute, then whisk in 1 cup of milk until smooth. Pour in remaining milk and whisk again. Bring the sauce just to a simmer.
Stir in nutmeg, Worcestershire sauce, and salt; simmer on medium-low heat until thickened, about 8 minutes, whisking often. Turn heat off, then add 2 1/4 cups of Cheddar cheese; stir until melted and combined. Add Dijon mustard.
Transfer the macaroni into a casserole dish, then pour in the cheese sauce; stir to thoroughly combine sauce with pasta. Mix panko bread crumbs and 1 tablespoon melted butter in a small bowl, and sprinkle crumbs on top of macaroni and cheese. Sprinkle remaining 3/4 cup of Cheddar cheese on top.
Bake in the preheated oven until bread crumbs and Cheddar cheese topping are golden brown, about 20 minutes.