Preheat the oven to 375°F. Stand the hollowed peppers upright in a baking dish, trimming the bottom flat if needed.
Cook the macaroni until just shy of al dente. Drain and set aside.
Melt the butter, whisk in the flour, and cook about 1 minute.
Slowly whisk in the milk and simmer until it coats the back of a spoon, about 4 minutes.
Off heat, stir in the cheddar and mozzarella until melted. Stir in mustard, garlic powder, nutmeg, salt, and pepper.
Fold in the drained macaroni, then spoon the mixture into the peppers.
Top with the panko-oil mixture. Cover and bake 20 minutes, then uncover and bake 10 to 15 minutes more until golden.
Rest 5 minutes before serving.