Preheat oven to 350°F (177°C) and lightly grease a 2-quart baking dish (9x9 or 8x8 inch square pan). Cook macaroni in salted boiling water for 6-7 minutes, about 1 minute less than package directions. The pasta will continue cooking in the oven. Drain thoroughly and set aside.

Melt 3 tablespoons butter in a medium saucepan over medium heat. Whisk in flour and cook for 60-90 seconds, stirring constantly until the mixture turns light golden and smells slightly nutty.

Gradually pour in milk in a slow, steady stream while whisking continuously. Continue whisking for 4-5 minutes until mixture thickens noticeably and coats the back of a spoon in a thin, even layer.

Reduce heat to low or remove pan from heat entirely. Add cheddar first, stirring gently until about 80% melted, then add mozzarella, and finally stir in 1/2 cup Parmesan. Work in batches and stir slowly to prevent the cheese from seizing. Season with garlic powder, onion powder, paprika, salt, and pepper.

Fold cooked macaroni into cheese sauce using a rubber spatula until every piece is coated. Transfer to prepared baking dish and spread evenly, pressing down lightly to eliminate air pockets.

Combine panko breadcrumbs with 2 tablespoons melted butter and remaining 1/4 cup Parmesan. Mix with a fork until crumbs are evenly coated, then sprinkle in an even layer over mac and cheese.

Bake for 25-30 minutes until top is golden brown and cheese sauce is bubbling around edges. Let rest 5-10 minutes before serving to allow sauce to set properly.