Bring a large pot of salted water to a boil over high heat.Add pasta and cook according to directions; drain well and set aside.
In a large deep skillet over medium heat, add clarified butter. When hot, add onions and sauté until translucent about 3 minutes. Add flour and stir well making sure the onions are coated. Cook onion/flour mixture a little, about 2-3 minutes, stirring constantly.
Pour in 1 cup cold milk and stir until smooth. Add the remaining 2 cups milk, stir well and then add mustard, paprika, garlic powder, cayenne pepper and nutmeg; stir again. Whisk in the two cheeses until melted; taste and adjust if necessary.
Add cooked and drained macaroni and gently combined into the cheese mixture. Turn up the heat to medium-high and bring the mixture to a simmer. Reduce heat to medium and cook for 5 minutes, stirring often. When ready to serve, sprinkle some fresh chopped parsley.