Prepare the pecan pie filling: In a small 1-quart stainless steel saucepan, combine all the filling ingredients except for the chopped pecans. Whisk the mixture until fully blended, then stir in the pecans. Place the saucepan over medium heat and cook, whisking constantly, until the mixture just begins to bubble and thicken. Let it bubble for an additional 30 seconds while continuing to whisk—this process should take about 5 to 7 minutes. Remove from heat immediately and pour the mixture into a clean bowl. Allow it to cool completely at room temperature, then transfer to the refrigerator and chill for about 1 hour until fully set and cold.

Prepare the cookie dough: In a large mixing bowl, combine the softened butter, granulated sugar, and brown sugar. Cream together using a wide rubber spatula by hand or beat with an electric hand mixer on medium speed for about 2 minutes, until the mixture is light, pale, and fluffy. Add the egg yolk and vanilla extract, mixing thoroughly, then stir in the milk until incorporated.

In a separate medium bowl, whisk together the flour, baking soda, baking powder, and salt until well blended. Gradually add the dry ingredients into the butter mixture, folding with a spatula until everything is evenly incorporated and the dough becomes smooth.

Cover the bowl and refrigerate the dough, or, for easier portioning later, transfer the dough onto a large sheet of plastic wrap. Using floured hands, shape and roll it into a 10-inch log. Wrap tightly and refrigerate for 1 hour or freeze for 30 minutes to firm up.

Line two large cookie sheets with parchment paper. If the dough was kept in the bowl, use a 1-ounce cookie scoop (about 2 tablespoons of dough) to portion out exactly 13 equal-sized cookies. Roll each scoop into a smooth ball. If using the dough log, slice it into 13 even pieces, roll each into a ball, and place on the prepared sheets, spacing them about 3 inches apart.

Using a 1-teaspoon measuring spoon, press down in the center of each dough ball to create a deep well. Gently push the sides upward or squeeze the dough slightly inward to maintain the shape. If any cracks appear in the dough, simply press them back together. Fill each well with about 1 teaspoon of the chilled pecan filling. You won’t need all the filling at this stage—save the remainder for topping the cookies after baking. Place the trays in the refrigerator for 15 minutes while preheating the oven.

Preheat the oven to 375°F (190°C).

Bake the cookies for 8 to 10 minutes, or until the edges are golden brown and the pecan filling starts to bubble. Remove the trays from the oven and place them on wire racks to cool for 5 minutes, then carefully transfer each cookie to the rack to cool completely.

Once the cookies have cooled, spoon a little of the reserved pecan filling on top of each one. If desired, sprinkle with additional chopped pecans for extra crunch. For an elegant finish, drizzle melted dark chocolate over the tops—this step is optional but adds a decadent touch.