In a small saucepan, combine all filling ingredients except the pecans. Whisk together until smooth, then add the pecans. Cook over medium heat, whisking constantly until it thickens and bubbles slightly, about 5-7 minutes. Remove from heat, transfer to a bowl, and chill in the refrigerator for about 1 hour.
Cream together softened butter, granulated sugar, and brown sugar until pale and fluffy. Add the egg yolk, vanilla, and milk, mixing well. In a separate bowl, combine flour, baking soda, baking powder, and salt. Fold the dry ingredients into the butter mixture until smooth.
Chill the dough for 1 hour or shape it into a log, wrap in plastic, and chill for 30 minutes in the freezer.
Preheat your oven to 375°F (190°C) and line two baking sheets with parchment paper.
Scoop out the dough and roll it into balls, placing them on the baking sheets. Make an indent in each cookie with a teaspoon, then fill each indent with the pecan pie filling. Refrigerate the trays for 15 minutes.
Bake for 8-10 minutes until golden brown. Let them cool on a wire rack for 5 minutes before transferring.
Once cooled, top each cookie with a bit of the remaining pecan pie filling and additional chopped pecans. Drizzle with melted dark chocolate if desired.
Notes
For a festive touch, sprinkle some sea salt on top of the cookies before baking.