01 - In a medium saucepan over medium heat, melt the butter and cook, swirling frequently, until foaming subsides and it develops golden color with brown flecks and a nutty aroma, about 5 to 7 minutes. Remove from heat and transfer to a large heatproof bowl. Allow to cool for 10 minutes.
02 - Whisk both brown sugar and granulated sugar into the cooled brown butter until fully blended. Add eggs and vanilla extract, whisking until the mixture is smooth and glossy.
03 - Stir in whole milk until incorporated.
04 - In a separate bowl, whisk together all-purpose flour, baking soda, and fine sea salt. Gradually fold the dry mixture into the wet ingredients until just combined; do not overmix.
05 - Gently fold in semisweet chocolate chips and 1 1/2 cups chopped salted pretzels, reserving the remaining pretzels for topping.
06 - Cover the dough and refrigerate for at least 30 minutes or up to 24 hours to enhance flavor.
07 - Preheat the oven to 350°F. Line two baking sheets with parchment paper.
08 - Scoop 2-tablespoon portions of dough onto prepared baking sheets, spacing them 2 inches apart. Press a few reserved pretzel pieces onto each dough ball and sprinkle with flaky sea salt if desired.
09 - Bake for 11 to 13 minutes, until edges are golden and centers appear just set. Let cookies cool on the pan for 5 minutes, then transfer to a wire rack to cool completely.