Heat oven to 375 degrees. Bring a large pot of lightly salted water to a boil. Add macaroni and cook 8 minutes or as per package directions. Drain and return to pot.
Meanwhile, melt butter in a saucepan over medium heat. Add flour and cook 1 minute. Whisk in milk in a thin stream. Whisk in mustard, onion powder, salt, pepper, nutmeg and cayenne. Bring to a simmer; cook 3 minutes, whisking occasionally.
Remove from heat and whisk in American cheese and 1 cup of the cheddar cheese. Whisk a little of the cheese sauce into the egg to temper. Whisk egg mixture back into cheese sauce.
Stir sauce into macaroni. Coat indents of 16 standard muffin cups with nonstick cooking spray. Divide macaroni among prepared cups. Top each with 1 tbsp of the remaining cheddar cheese. Bake at 375° for 18 minutes until lightly browned. Cool slightly before running a thin spatula around edge and spooning out of pans.