Brown the butter in a light-colored saucepan over medium-low heat, swirling occasionally until amber with brown bits forming, about 8 to 10 minutes, then transfer it immediately to a heat-safe bowl and let it cool slightly.
Toast the pecan halves with the other 2 tablespoons of butter in a skillet over medium heat, stirring constantly until glossy and fragrant, about 2 minutes, then transfer them to a cutting board to cool and roughly chop them. Set your buttered pecans aside for later.
Preheat the oven to 350°F and line baking sheets with parchment paper.
Mix the granulated sugar, the brown sugar, and the cooled browned butter in the bowl of a stand mixer fitted with the paddle attachment until smooth and well combined.
Add the eggs, the vanilla, and the bourbon, mixing well and scraping down the bowl so everything is evenly incorporated.
Add the flour, the baking soda, the salt, the cinnamon, and the cream of tartar, mixing just until a thick dough forms and no dry flour remains.
Fold in the chocolate chips and the buttered pecans with a silicone spatula to avoid overmixing.
Portion the dough into even mounds with a large cookie scoop and place them on the prepared baking sheets with at least 2 inches between each.
Bake the cookies for 12 to 14 minutes until the edges are lightly browned and the centers are just set.
Cool the cookies briefly on the baking sheet, transfer them to a wire rack, and sprinkle with flaky sea salt while still warm if desired.