Preheat oven to 325 degrees (F). Line two large baking sheets with parchment paper, lightly spray them with non-stick spray, and set aside.
In a medium bowl, whisk together the all-purpose flour, unsweetened cocoa powder, baking powder, and salt; set aside.
In a large, microwave-safe bowl, combine one cup of the semi-sweet chocolate chips and the unsalted butter. Heat them in the microwave on low power, in 15-second increments, mixing in between each, until butter and chocolate are completely melted and can easily be whisked smooth.
In a large bowl, whisk together both granulated sugar and light brown sugar with the eggs, beating until well combined. Beat in whole milk and vanilla extract. Then fold in the melted chocolate, stirring until evenly combined.
Using a rubber spatula, fold the dry ingredients into the wet ingredients, stirring just until combined. Do not over mix here!
Fold in the remaining semi-sweet chocolate chips, stirring until everything is just combined.
Scoop 1/4 cupfuls of the batter directly onto the prepared baking sheets, leaving room for spreading.
Bake one tray at a time for 15 minutes, or until the edges are set and the tops are dark and shiny.
Press a few extra chocolate chunks on top of the warm cookies and sprinkle with flaky sea salt.
Allow cookies to completely cool on the baking sheet for one hour before serving!