Preheat oven to 350 degrees F.
To make the buttered pecans, melt 1 ½ tablespoons of butter in a large skillet over medium heat. Add chopped pecans to the skillet and stir to coat in the butter. Allow the pecans to toast for about 5 minutes, stirring occasionally. Turn off the heat and set aside.
To brown the butter, add 1 cup of butter to a medium skillet on medium heat. Stir frequently and cook just until the butter turns an amber color with brown bits at the bottom of the pan. Promptly remove the skillet from the heat and pour browned butter into a bowl and set aside.
In a large mixing bowl, add gluten-free flour, salt, baking powder, and baking soda. Whisk to combine and set aside.
In a separate large mixing bowl, add cooled brown butter, brown sugar, and granulated sugar. Use a hand mixer to cream together.
Add bourbon and vanilla extract and mix until incorporated.
Add eggs, one at a time, mixing for about 15 seconds each time.
Fold the flour mixture into the batter, stirring just until combined.
Fold in the dark chocolate chips and chopped buttered pecans.
Use a ¼ cup cookie scoop to scoop the batter onto a large baking sheet, leaving about 3 inches between cookie dough balls.
Use clean hands to gently flatten each cookie dough ball. Decorate by adding a few additional chopped pecans and chocolate chips to each cookie.
Bake in preheated oven for 10-12 minutes or until golden brown. Sprinkle flaky sea salt onto each freshly baked cookie. Allow the cookies to remain on the baking sheet for 2 minutes before transferring them to a cooling rack.