Preheat the oven to 400 degrees F (200 degrees C).
Bring a large pot of lightly salted water to a boil. Cook elbow macaroni in the boiling water, stirring occasionally, until tender yet firm to the bite, about 8 minutes. Drain and set aside.
Melt 1/4 cup butter in a large saucepan over medium heat. When butter starts to foam and bubble, stir in flour; cook on medium heat until flour begins to turn pale yellow, 3 to 4 minutes.
Add thyme, cayenne, and white pepper; cook and stir another minute, then whisk in 1 cup milk until smooth. Pour in remaining milk and whisk again. Bring sauce just to a simmer.
Stir in salt, Worcestershire sauce, and nutmeg. Simmer, whisking often, on medium-low heat until thickened, about 8 minutes.
Turn heat off, then add 2 1/4 cups Cheddar cheese; stir until melted and combined. Mix in Dijon mustard.
Transfer macaroni into a 8x8-inch casserole dish, then pour in cheese sauce; stir to thoroughly combine pasta with sauce.
Mix together panko bread crumbs and 1 tablespoon melted butter in a small bowl.
Sprinkle mixture over macaroni and cheese. Sprinkle remaining 3/4 cup Cheddar cheese on top.
Bake in the preheated oven until top is golden brown, about 20 minutes.
