In a medium mixing bowl, vigorously whisk together the all-purpose flour, natural cocoa powder, baking soda, baking powder, and kosher salt until fully combined with no cocoa clumps.

In the bowl of a stand mixer, beat the melted, slightly cooled butter, light brown sugar, and granulated sugar on medium speed for 2 minutes. Add the whole egg, extra egg yolk, and vanilla extract. Beat for another 2 minutes until pale and ribbon-like.

Add the red gel food coloring and white vinegar. Mix on low speed until a vibrant crimson red color is fully incorporated. Scrape down the sides of the bowl.

Pour the dry ingredients into the wet mixture. Mix on the lowest speed just until the flour streaks disappear to maintain a tender crumb.

Cover the bowl tightly with plastic wrap and chill in the refrigerator for at least 2 hours to prevent spreading during baking.

Preheat your oven to 350°F (175°C). Line two baking sheets with parchment paper.

Using a 3-tablespoon cookie scoop, portion the chilled dough into tall mounds. Space them 3 inches apart on the baking sheets.

Bake for 11 to 13 minutes until the edges are set and the tops show a slightly cracked, crinkled surface with a fudgy center.

Allow the cookies to cool directly on the hot baking sheet for 10 minutes before transferring them to a wire rack to cool completely.