Preheat oven to 375°F; lightly grease a 9x13-inch dish.
Cook macaroni according to package just shy of al dente, about 6 minutes; drain and set aside.
Melt butter in a large saucepan over medium; whisk in flour and cook 1 minute until golden and bubbly.
Gradually whisk in milk; cook about 5 minutes until thickened, stirring constantly.
Remove from heat; stir in cheddar, Gruyere, garlic powder, salt, and pepper until smooth.
Fold in macaroni until combined.
Arrange pepper halves in dish; fill generously with macaroni mixture.
Sprinkle each with panko.
Cover with foil; bake 25 minutes. Uncover; bake another 10 minutes until peppers are tender and tops golden brown.