In a large mixing bowl, whisk together the flour, sugar, baking powder, baking soda, salt, and black pepper until thoroughly combined. Add the dehydrated onion flakes and whisk again to distribute evenly throughout the dry ingredients.
Remove the cold butter from the refrigerator. Using a box grater, grate the butter directly over the dry ingredients. Toss the grated butter with the flour mixture using your hands until all butter pieces are coated in flour. Cut butter in with a pastry cutter or fork.
Add the 100 grams of shredded smoked cheddar to the bowl and toss to coat the cheese in the flour mixture as well. Place the entire bowl in the freezer for 15 minutes. Chilling the butter and cheese together ensures both stay cold through mixing and create distinct pockets in the finished scone.
While the bowl is in the freezer, prepare your wet ingredients using one of two methods. Method 1 (blended, guaranteed smooth): Add cottage cheese to a blender/ food processor or use an inversion blender and blend for 30 to 60 seconds until completely smooth. Add the cold egg and cold sourdough discard and pulse briefly for 10 to 20 seconds until just combined. Do not over-process. Method 2 (whisked, for Good Culture, Nancy’s, or Daisy): Whisk all wet ingredients together in a medium bowl. If using Daisy brand, use a fork or immersion blender to break up the larger curds before whisking in the remaining ingredients. Keep the wet ingredients in the refrigerator until the freezer timer goes off. Remove the bowl from the freezer. Pour the dry ingredients over the wet ingredients. Using a rubber spatula, fold gently until a shaggy, rough dough forms. The dough will look clumpy. Do not add more flour and do not overmix. Since there is such a difference in cottage cheese hydrations, if your dough would seem too dry, add 1 Tablespoon (14 grams) of buttermilk or milk at a time.
Line an 8 by 8 inch square pan with parchment paper, leaving overhang on two sides. Transfer the dough to the pan and press evenly to a 1 inch height, making sure the edges are the same thickness as the center.
Cover the pan tightly with plastic wrap and refrigerate for 8 to 12 hours. You can skip the long ferment and refrigerate for only 2 hours until the dough firms back up.
Preheat the oven to 425 degrees Fahrenheit (218 C). Use the parchment overhang to lift the slab out of the pan and onto a cutting board. Cut into 9 equal squares using a sharp knife in a 3 by 3 grid pattern. Transfer the squares to a parchment lined baking sheet, spacing them about 2 inches apart.
Sprinkle the reserved 25 grams of shredded smoked cheddar evenly over the top of the dough.
Place in the freezer for 30 minutes to an hour.
Place the frozen scones directly into the preheated oven. Reduce the temperature to 375 degrees Fahrenheit. (190 C)
Bake for 20 - 25 minutes, until the tops are deep golden and the smoked cheddar on top is bubbling and set. The scones are done when an instant-read thermometer inserted into the center reads 200 degrees Fahrenheit.
Remove from the oven and allow the scones to cool on the baking sheet for 5 minutes before serving. They are best served warm.