Preheat oven to 375°F and lightly grease a 9x13-inch baking dish.
Cook macaroni according to package directions until just shy of al dente, about 6 minutes. Drain and set aside.
In a large saucepan, melt butter over medium heat. Whisk in flour and cook for 1 minute until golden and bubbly.
Gradually whisk in milk and cook, stirring constantly, until sauce thickens, about 5 minutes.
Remove from heat and stir in cheddar cheese, Gruyere, garlic powder, salt, and pepper until smooth.
Fold cooked macaroni into the cheese sauce until well combined.
Arrange pepper halves in the prepared baking dish and fill each generously with mac and cheese mixture.
Sprinkle panko breadcrumbs over the top of each stuffed pepper.
Cover with foil and bake for 25 minutes, then remove foil and bake an additional 10 minutes until peppers are tender and tops are golden brown.