Position a rack in the center of the oven and heat the oven to 325°F.
Put the pork in a large heavy-duty roasting pan, cover with foil, and roast until the meat is falling off the bone, 5 to 6 hours. Cool until warm enough to handle, about 1 hour.
Meanwhile, cook the pasta in a large pot of well-salted water according to package directions until just barely al dente. Drain and set aside.
Shred the pork by hand, pulling it into 2-inch-long pieces. Discard the bone and any excess fat. Set aside 1 lb. of the pulled pork (about 4 cups) and save the rest for another use (see "Leftovers," below, for ideas).
Raise the oven temperature to 350°F. Melt the butter in a large 8-quart saucepan over medium heat. Add the onions, reduce the heat to low, and cook, stirring frequently, until golden and very soft, about 20 minutes.
Whisk in the flour and cook for 30 seconds. Whisk in the milk in a slow, steady stream. Raise the heat to medium high and whisk constantly until the mixture begins to thicken and bubble, 3 to 5 minutes.
Whisk in the white wine, sage, and a 1/2 tsp. each salt and pepper. Bring the mixture to a low simmer, whisking constantly.
Reduce the heat to low and use a wooden spoon to stir in the Gruyère, Emmentaler, and fontina. Stir in the reserved pork and pasta until well coated. Pour the mixture into a 12-inch cast-iron skillet.
In a small bowl, mix the panko, Parmigiano, and olive oil. Sprinkle evenly over the mixture in the skillet.
Bake until the topping is browned and the cheese sauce is bubbling through the topping and around the edges of the skillet, 40 to 45 minutes. (If the topping begins to brown too deeply, tent loosely with foil.) Let the macaroni and cheese rest for at least 15 minutes. Sprinkle with the chives and serve.