Measure out the milk and sour cream and allow them to sit on your counter to come to room temperature (20 to 30 minutes).
Arrange a rack in the middle of the oven. Preheat the oven to 425ºF/218ºC. Grease a standard 12-cup muffin tin on the bottoms and sides with coconut oil or cooking spray–be generous to avoid sticking.
In a small bowl, whisk together the flaxseed meal and 4 tablespoons of warm water. Set aside for 10 to 15 minutes to gel up.
Add one tablespoon of apple cider vinegar to the milk and stir. This creates the "buttermilk". Stir and set aside for 5 to 10 minutes.
Chop the chocolate (not too finely). Set aside ¼ cup (~30g) of the chopped chocolate or chocolate chips for the topping.
In a medium bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon and nutmeg.
In a large bowl, whisk together the flax eggs, melted butter, and sugar until combined. Then whisk in the sour cream, buttermilk and vanilla extract. It’s okay if there are tiny chunks of sour cream unblended.
Add the dry ingredients to the wet. Gently fold together until JUST combined, do not overmix. The batter will be thick and not runny. Some clumps are okay. Gently fold in the chocolate with a silicone spatula.
Fill the muffin tins nearly to the top with the batter. Sprinkle a bit of the coarse sugar on top of each muffin and press the reserved chocolate pieces or chips into the tops.
Bake at 425ºF/218ºC for 6 minutes. Then, without opening the oven door, reduce the heat to 350ºF/175ºC and bake for another 16 to 20 minutes, or until a toothpick comes out clean or with a few crumbs.
Transfer to a cooling rack and cool for 20 to 30 minutes. Use a small offset spatula or butter knife to loosen the muffins. Store cooled muffins in an airtight container on the counter for 2 to 3 days, or in the fridge for 5 to 6 days, or up to 3 months in the freezer.