Heat oven to 400°. Cook pasta according to package directions but stop about 2 minutes less than al dente since it will keep cooking as the dish bakes; drain and set aside.
Melt 2 tablespoons butter in large saucepan over medium heat. Add onion and sauté until just starting to brown; add garlic, and cook for 1 minute. Slowly sprinkle flour over butter and cook, stirring constantly, about 1 minute. Flour should start to smell slightly nutty but not brown. Add 2 cups milk and whisk until smooth. Let sauce come to a low boil, reduce temperature and let sauce simmer until slightly thickened. If too thick, add up to 1 cup more cup milk and bring to a low boil (as sauce cooks, it will thicken). Season lightly with salt and pepper, Old Bay, and nutmeg. Remove pan from heat and stir in cheese, stirring until sauce is smooth and creamy. Combine sauce with macaroni, seafood, 1 tablespoon parsley, chives, and red peppers; transfer mixture to a buttered shallow 4-quart baking dish.
Place breadcrumbs in a metal bowl with remaining tablespoon fresh parsley and a pinch or two of Old Bay. Melt remaining 2 tablespoons butter, pour over breadcrumb mixture and toss to combine. Sprinkle breadcrumb-butter mixture over top of macaroni and bake until top is golden and sauce is bubbling, 15 to 20 minutes. Let cool 5 minutes before serving.