Preheat the oven to 350°F. Line a baking sheet with parchment paper.
Make the Pecans: Toss the pecans with maple syrup and brown sugar. Spread on the prepared baking sheet and bake for 15 minutes, until caramelized. Drizzle with bourbon, if using. Let cool, then roughly chop 1 cup, including the caramelized bits. Reserve the remaining pecans for topping.
Make the Cookies Brown the butter in a skillet over medium heat, swirling until golden, 2–4 minutes. Transfer to a bowl. Whisk in the brown sugar, granulated sugar, egg, egg yolk, and vanilla. Add the flour, baking soda, and salt. Mix until just combined. MIx in the chocolate chips and chopped pecans.
Arrange 18 Original Pretzel Crisps on a parchment-lined baking sheet. Roll the dough into rounded 1-tablespoon balls and place one on top of each pretzel. PLace a pecan on top. Freeze for 10 minutes.
Bake for 6 minutes. Rotate the pan and gently tap it on the counter to flatten the cookies. Bake for 2–3 minutes more, until the edges are set and the centers are slightly glossy. Don't overbake!
Let cool on the baking sheet. Drizzle or dip in melted chocolate, then finish with the remaining maple pecans and flaky sea salt. Enjoy!