Preheat oven to 375˚F. Lightly grease a large casserole dish.
In a large frying pan, melt butter over medium low heat. Add the onions, season with a pinch of salt, and cook, stirring occasionally, until golden brown and caramelized. This will take about 30 minutes.
Bring large pot of salted water to a boil.
Once water comes to a boil, add the cubed potatoes. As they begin to soften, after about 5 minutes, add the dried penne. Continue to cook, stirring occasionally, until potatoes are tender and pasta is barely tender, about 7 minutes. The pasta will cook a little further as it bakes. Drain and set aside.
In a medium bowl, season cream with salt, pepper, and about 1/4 teaspoon freshly grated nutmeg.
Add 1/3 of penne and potatoes to the bottom of prepared dish. Evenly cover with 1/3rd of the grated cheese. Top with another 1/3 of penne and potatoes. Top with another 1/3rd of the cheese, then remaining penne and potatoes. Top evenly with the remaining shredded cheese. Pour the seasoned cream over the layers.
Bake in preheated oven until heated through and the cheese is melted and bubbly, about 15-20 minutes. Remove from the oven and evenly top with the caramelized onions.
Serve the Älplermagronen hot either over the applesauce or with the applesauce on the side. If desired, top with a little fresh parsley or chives.