01 - Melt unsalted butter in a medium saucepan over medium heat. Swirl occasionally while cooking until the butter foams and develops a golden brown color with a nutty aroma, approximately 5 minutes. Transfer browned butter to a large mixing bowl and allow to cool for 10 minutes.
02 - To the cooled brown butter, add light brown sugar, granulated sugar, and honey. Whisk thoroughly until all ingredients are fully incorporated. Beat in eggs one at a time, then stir in pure vanilla extract until smooth.
03 - In a separate bowl, whisk together all-purpose flour, baking soda, baking powder, and fine sea salt until evenly combined.
04 - Gradually stir dry mixture into the wet ingredients just until combined. Avoid over-mixing.
05 - Fold in semi-sweet chocolate chips and crushed mini salted pretzels, reserving a small amount of each for topping the cookies.
06 - Cover dough and refrigerate for a minimum of 30 minutes, or up to 24 hours for enhanced flavor.
07 - Preheat oven to 350°F. Line two baking sheets with parchment paper.
08 - Scoop 2-tablespoon portions of dough onto prepared baking sheets, spacing each portion 2 inches apart. Press reserved chocolate chips and pretzel pieces gently into the tops of each mound.
09 - Bake cookies for 11 to 13 minutes, or until edges appear golden and centers are just set.
10 - Remove baking sheets from oven and immediately sprinkle cookies with flaky sea salt. Allow cookies to cool on sheets for 5 minutes before transferring to a wire cooling rack to cool completely.