Preheat oven to 425˚F (220˚C). Grease 36 mini muffin cavities.
Bring a large pot of salted water to a boil. Cook the pasta, stirring occasionally, until barely tender, al dente. Drain and set aside.
While the pasta is cooking, melt the butter in a large saucepan over medium heat.
Once melted, mix in the flour and cook until golden, whisking constantly.
Slowly pour in the milk while whisking. Cook, whisking often, until thickened.
Stir in the salt, paprika, pepper, garlic powder, and onion powder.
Remove from heat, the add the Cheddar, Gruyère, and Parmesan cheese a handful at a time, stirring well between each addition.
Mix in the egg yolks, then fold in the cooked pasta until well coated.
Fill each of the prepared muffin tins with the pasta. Do not overfill.
Sprinkle the panko over each macaroni and cheese bite, then sprinkle some grated Parmesan cheese.
Bake in the preheated oven until the macaroni bites are bubbly and golden around the edges, about 12 minutes.
Allow to cool in the pan for 10 minutes before removing with a small spoon or off-set spatula.
Garnish with freshly chopped parsley or chives before serving.