Add the bacon to a large Dutch oven and cook over medium heat until crisp. Transfer the bacon to a paper towel-lined plate, leaving about 2 tablespoons of bacon drippings in the Dutch oven.
Add the onions to the bacon drippings. If the Dutch oven seems dry, add the butter. Cook over medium-low heat for about 15 minutes, stirring occasionally, until the onions are very soft and deep golden brown. Transfer the onions to a plate and set aside.
Bring a large pot of well-salted water to a boil. Add the potatoes and cook for about 2 minutes. Add the pasta and continue cooking until the pasta is just barely al dente and the potatoes are fork tender. Cook the pasta about 1 minute less than the package directions. Before draining, reserve at least 1 cup of the pasta cooking water.
Add the drained pasta and potatoes to the Dutch oven. Pour in the heavy cream and ½ cup of the reserved pasta water. Heat gently over medium-low heat, stirring occasionally, just until everything is hot. Do not let the cream come to a boil.
Remove the Dutch oven from the heat. Reserve about 1 cup of the shredded Gruyère and Emmentaler for the top. Add the remaining cheese a handful at a time, gently stirring until melted and creamy.
Stir in about two-thirds of the bacon and caramelized onions. Add the black pepper and nutmeg. Add additional pasta water a few tablespoons at a time until the sauce is very creamy and slightly looser than you want the finished dish to be.
Sprinkle the reserved cheese evenly over the top. Place the Dutch oven in the oven about 5 to 6 inches below the broiler. Broil for 2 to 4 minutes, watching closely, until the cheese is melted and browned in spots. Sprinkle the remaining bacon and caramelized onions over the top.
Let the Älplermagronen rest for about 5 minutes before serving. Serve hot with cold or room-temperature applesauce on the side.