For the filling: Heat the butter in a medium skillet over medium heat. Add 1/2 teaspoon of the salt, the thyme, onions and apples and cook until the apples and onions soften, about 5 minutes. Stir in the garlic and continue cooking for 2 more minutes. Remove from the heat, discard the thyme, and let the mixture cool completely.
Toss together the cooled apple-onion mixture, pork butt, bacon, sage, black pepper, mace, nutmeg, white pepper and remaining 1 1/2 teaspoons salt in a large bowl. Transfer half the mixture to a food processor and pulse until it starts to forms a paste, about 10 times, and then return to the bowl and mix well with the chunkier pieces. Refrigerate while you make the dough.
For the dough: Place the flour in a large bowl. Heat the butter, lard and salt with 2/3 cup water in a small saucepan until the butter and lard melt, and then add into the flour. Mix until a smooth dough forms. While the dough is still warm, create the pie shells by pressing 1/4 cup of the dough into each ramekin so that it covers the bottoms and sides and spreads all the way up past the top. Make sure there are no holes and the dough is the same thickness throughout, about 1/8-inch thick. Divide the remaining dough into 6 equal pieces and roll out to form circles larger than the ramekin width (about 4 inches in diameter) to cover the pies. Cut out a small vent hole in the middle of each.
Place a baking sheet on the bottom rack of the oven. Preheat the oven to 425 degrees F.
Fill each ramekin with about 1/2 cup of the meat filling. Brush the beaten egg yolk on the top of the dough overhang on the edges of the ramekin, being careful not to get egg wash on the ramekin. Brush egg wash on the edges of the dough circles, and then cover the ramekins with the lids egg-wash-side down. Trim off any excess dough with kitchen shears and press down the edges with the tines of a fork. Brush the tops with more egg wash.
Place the ramekins on the hot baking sheet in the oven. Bake on the bottom rack 20 minutes, and then turn down the heat to 375 degrees F and continue baking until golden brown and slightly puffed, 25 to 30 minutes longer.
Let the pies cool completely before carefully popping them out of the ramekins. Serve at room temperature with mustard on the side.