Preheat the oven to 375°F. Grease two mini muffin pans with nonstick cooking spray.
In a large pot of boiling salted water, cook the pasta al dente according to package instructions, about 7–9 minutes. Drain and set aside to cool.
In a large saucepan over medium heat, melt the butter. Add the flour, garlic powder, mustard powder, salt and pepper, and stir to combine, about 2 minutes. Add the milk and whisk well to combine. Bring the mixture to a simmer over medium-low heat, stirring occasionally for 5 minutes.
Remove the pot from the heat and add the cheese, stirring until melted. Fold the cooked pasta into the pot, or pour the cheese over the cooked pasta in a large bowl, and stir until evenly coated.
Scoop about 2 tablespoons of the mac and cheese mixture into each prepared muffin cup. Pack it in with the back of a spoon to help the bites hold their shape. Sprinkle panko breadcrumbs on top.
Bake until the cheese melts and the breadcrumbs are golden, 20–25 minutes.
Cool the bites for 5–10 minutes before removing from the muffin cups and serving.