Preheat your oven to 425°F (220°C). Line a muffin tin with paper liners or grease it lightly with oil. Spray the paper liners lightly with non-stick spray.
In a blender or food processor, blend cottage cheese, and applesauce. Then add to a large bowl with remaining wet ingredients, including olive oil, cane sugar, apple cider vinegar, and vanilla extract and whisk until smooth.Add the 3 large eggs and mix until well combined. Add the dry ingredients, including oat flour, almond flour, cocoa powder, baking powder, cinnamon, and salt and whisk until just combined. Do not overmix. Gently fold in chocolate chunks with a spatula.
Divide the batter evenly among the prepared muffin cups, filling each about 2/3 full. Press a few additional chocolate chips into the tops of the muffins.Bake at 425°F for 5 minutes. Then, leave the muffin tin in the oven, reduce the heat to 350°F (180°C), and bake for 14-16 minutes, or until a toothpick inserted into the center of a muffin comes out clean. Allow the muffins to cool in the tin for about 5 minutes, then transfer them to a wire rack to cool completely. Blend cottage cheese, maple syrup, cocoa powder, vanilla extract, and salt until smooth.
Using a spoon with a thin handle, gently press a hole in the center of each muffin to create a narrow cavity. Pour the sauce and fill the cavity to the top. Serve the muffins warm or wait until cool and set.