Move an oven rack to the center position and preheat the oven to 350°F (175°C). Place 24 mini cupcake liners into a 24-cup mini muffin pan, pressing each liner down gently so it sits flat.
Spread the chopped pecans and pecan halves in a single layer on a rimmed baking sheet. Toast for 6 to 8 minutes, stirring once halfway through, until nutty and slightly darker. Transfer to a cool plate and leave the oven on at 350°F.
Cut the butter into pieces and melt gently in a small saucepan over low heat or in a microwave-safe bowl in 20-second bursts. Cool for about 5 minutes so it is warm, not hot.
Pour the melted butter into a large mixing bowl. Add the brown sugar and maple syrup, then whisk for about 1 minute until smooth and glossy with no dry clumps of sugar.
Add the whole egg, extra egg yolk, and vanilla extract. Whisk vigorously for 1 to 2 minutes until the batter looks thick, shiny, and slightly lighter in color.
In a medium bowl, combine the flour, baking powder, and salt. Whisk for about 20 seconds so the baking powder and salt are evenly spread through the flour.
Add the flour mixture to the wet ingredients and fold gently with a silicone spatula until no dry streaks of flour remain. Fold in the toasted chopped pecans until evenly spread through the batter.
Use a 1 tablespoon cookie scoop to portion the batter into the lined cups, filling each about three-quarters full. Press one toasted pecan half gently into the center of each mound of batter.
Bake on the center rack at 350°F for 11 to 13 minutes, until the edges are golden brown and the tops look set but still slightly soft in the middle. A toothpick inserted in the center should come out with a few moist crumbs.
Let the pan rest on a wire cooling rack for 5 minutes. Lift the bites out of the pan, still in their liners, and set them directly on the rack. Cool completely for about 20 minutes before glazing.
In a small bowl, whisk together the powdered sugar, maple syrup, and milk until completely smooth. Drizzle over the cooled bites, sprinkle with a tiny pinch of flaky sea salt, and let set for about 10 minutes before serving.