Preheat your oven to 350°F (175°C) and line a 9x9-inch baking pan with parchment paper, leaving some overhang for easy removal later.
In a large mixing bowl, combine the creamy cookie butter, light brown sugar, granulated sugar, and vanilla extract. Mix until well combined. Add in the egg, egg yolk, and molasses, whisking until the mixture is smooth and creamy.
In a separate bowl, whisk together the all-purpose flour, ground cinnamon, and salt. Gradually add the dry mixture to the wet ingredients, stirring until just combined.
Gently fold in the chopped semi-sweet chocolate chunks until evenly distributed throughout the batter.
Spread the batter evenly in the prepared baking pan. Bake for 25-30 minutes, or until the edges are golden and a toothpick inserted into the center comes out with a few moist crumbs.
Remove the bars from the oven and immediately sprinkle the remaining chocolate chunks on top. Allow the bars to cool in the pan for about 10 minutes before sprinkling with flaky sea salt.
Using the parchment overhang, lift the bars out of the pan and let them cool completely on a wire rack. Once cooled, slice into squares and enjoy!