In large pot of boiling salted water, add pasta and cook until al dente, about 7 minutes. Strain, rinse with cold water and set aside.
In medium skillet, pan-fry brats over medium-high heat for 3-5 minutes until browned on each side. Set aside.
In saucepan over medium heat, add 4 tablespoons butter, onion, pinch of salt, and red pepper flakes. Cook for a few minutes until onion becomes translucent and slightly caramelized. Whisk in 1 tablespoon flour and cook 2-3 minutes until tan-colored roux has developed. Whisk in heavy cream. Cook, stirring often, until mixture bubbles and begins to thicken; about 3 minutes. Add limburger, with rind still attached, and stir consistently so cheese melts into creamy and smooth sauce. Add whole grain mustard, honey, and apple cider vinegar, salt, and pepper and stir.
In pot, combine cooked pasta, brats, and limburger sauce and then transfer to baking dish. Season with salt and pepper. Place shaved red onions evenly across top and set aside.
Place rye bread in food processor. Pulse until tiny bread crumbs form. In small skillet over medium-high heat, melt remaining 1 tablespoon butter and add bread crumbs, salt and pepper. Stirring frequently, toast breadcrumbs until golden brown and fragrant. Pour rye breadcrumbs over macaroni and cheese and serve immediately.