Preheat oven to 350 degrees. Line two baking sheets with parchment paper.
Whisk together flour, cocoa, baking powder, and salt in a medium bowl.
Place chocolate and butter in a double boiler over gently simmering water. Slowly melt the chocolate, stirring occasionally until smooth. Remove from the heat and set aside to cool slightly.
Combine eggs, sugars, and vanilla in a large mixer bowl fitted with a whisk attachment and whisk together on medium speed for exactly 5 minutes. Reduce speed to low and beat in melted chocolate for 1 minute. Add flour mixture and mix on low speed for 20 seconds, just until combined. Fold in chocolate chips (dough will resemble a gooey brownie batter).
Use a cookie scoop lightly coated with nonstick spray to form the cookies. Invert the scoop just above the baking sheets, spacing cookies 3-inches apart.
Bake for 12 to 14 minutes, rotating pans halfway through, until tops are shiny and crackly.
Remove from oven and sprinkle with flaky salt. Allow cookies to cool for 10 minutes on baking sheets; transfer to a wire rack to cool completely.