►Melt 1 tablespoon butter in a large skillet over medium-low heat. When butter foams, add onion and a pinch of salt. Cook, stirring often, until onions are darkened and collapsed, about 20 to 30 minutes. Deglaze skillet with balsamic vinegar. Remove onions from skillet, chop, and set aside.
►Cook cavatappi half the time instructed on the package. Drain and set aside. Heat oven to 375°F.
►Combine brie and fontina in a large bowl and set aside. Melt 4 tablespoons butter in a large saucepan over medium heat. Add flour and cook until golden brown and nutty-smelling, about 2 to 3 minutes. Add thyme and garlic powder. Reduce heat to low. Whisk in milk in a slow stream. Add brie and fontina and whisk until melted and smooth.
►Meanwhile, melt remaining tablespoon of butter in a small skillet over medium heat. Add breadcrumbs and stir until all breadcrumbs are coated with butter. Remove from heat and add grated parmesan.
►Combine pasta and cheese sauce in a large bowl and stir to coat. Coat a 9-inch-by-13-inch glass baking dish with butter. Transfer mac and cheese to prepared baking dish. Top with breadcrumb mixture. Bake 15 to 20 minutes, or until top is golden and cheese is bubbling.