Prepare Hot Fudge Sauce in advance if using homemade. One batch of muffins uses about a 1/2 batch of this homemade fudge sauce.
In a large bowl, whisk together 1½ cups all-purpose flour, ½ cup Dutch Process cocoa powder, 2 tablespoons black cocoa powder, 2 tablespoons milk powder, 1 teaspoon salt, ¾ teaspoon baking soda, ½ teaspoon espresso powder, and ¼ teaspoon baking powder and set aside.
In a medium microwave-safe bowl, melt ½ cup salted butter.
Whisk in ⅓ cup + 1 tablespoon buttermilk, ¼ cup canola oil, and 1 tablespoon vanilla extract, then beat in the 2 large eggs one at a time.
Whisk in 1 cup vanilla skyr yogurt until smooth, then whisk in 1⅓ cups light brown sugar until fully incorporated.
Pour the wet ingredients into the bowl with the dry ingredients and whisk just until combined and no dry streaks remain - do not overmix.
Fold in 4 ounces dark chocolate and 4 ounces milk chocolate (chopped) until evenly distributed throughout the batter.
Cover the batter with a dish cloth and let rest for 30 minutes.
Meanwhile, preheat the oven to 425°F and line a regular muffin tin with tulip parchment liners. After the batter has rested, use a #16 scoop to portion out slightly heaping scoops of batter into the prepared muffin tin. You should have enough batter for 16 muffins and the batter just about fills to the rim of the pan (not the rim of the liner).
Top the muffins with additional chocolate chunks, you can go a little heavy-handed here, about 10 to 12 chunks per muffin is great!
Bake at 425°F for 7 minutes, then REDUCE heat to 350°F and bake for an additional 13 to 15 minutes or until a toothpick comes back mostly clean from the center (keep in mind that there is chocolate in the batter that is just going to melt and will leave some residue).
Remove from the oven and allow to cool for about 15 minutes in the pan, and bake off the remaining muffins if baking in batches.
Use the end of a wooden or silicone spatula to poke a hole in the top of each muffin.
Place the hot fudge in a piping bag, cut a ¼-inch hole in the tip, and pipe into the hole in the top of the muffins.