Preheat oven to 375 degrees F (190 degrees C). Line a baking sheet with parchment paper.
Stir the flour, sugar, baking powder, baking soda, and salt together in a mixing bowl. Use two forks or a pastry blender to cut in the shortening with the flour mixture until the mixture resembles coarse corn meal. Stir in the apples.
Whisk 1 egg, yogurt, milk, and almond extract together in a small bowl until smooth. Stir the egg mixture into the flour mixture just until blended. Gather the dough, and place the dough on a lightly floured surface; knead 4 to 5 times. Pat dough into a 7 inch diameter circle about 1 1/2 inch thick. Cut dough into 8 wedges, and place on prepared baking sheet.
To make the scone topping, whisk the milk and 1 egg together in a small bowl. Brush tops of scones with the egg mixture. Sprinkle each scone with cinnamon sugar and almonds.
Bake in preheated oven until tops are golden brown, and a toothpick inserted in center comes out clean, about 20 minutes. Remove from oven and cool on a wire rack. Serve warm or at room temperature.