Preheat the oven to 350°F and line a 12-cup muffin tin with paper liners, then lightly spray the liners with cooking spray.
Blend the oats in a blender until they become a fine flour, 30-45 seconds. Transfer to a large bowl and whisk in the protein powder, cocoa powder, baking powder, baking soda, espresso powder and salt.
Add the cottage cheese, eggs, maple syrup, brown sugar, melted butter and vanilla to the blender. Blend until silky smooth, 45-60 seconds.
Pour the wet mixture into the dry ingredients and fold until combined, then fold in 1/2 cup of the chocolate chips. Let the batter rest for 10 minutes so the oat flour hydrates and thickens, which gives you taller domes.
Divide the batter among the cups and top with the remaining 1/4 cup chocolate chips.
Bake for 17-20 minutes, just until the centers spring back when lightly pressed and a toothpick comes out with moist crumbs. Do not overbake, since protein powder dries out quickly.
Sprinkle with flaky sea salt while warm. Cool in the pan for 10 minutes, then move to a wire rack. The muffins get fudgier as they cool.