1. Toast whole almonds: Spread on a cookie sheet and bake at 350 degrees F, stirring once, 7 to 9 minutes.
2. Finely grind toasted almonds in a food processor or blender. Transfer to a large bowl and add whole-wheat flour, all-purpose flour, baking powder, and salt; stir until just combined. Beat 2/3 cup honey, the oil, and 3 Tbs. butter in a mixing bowl with an electric mixer on medium speed until well combined. Add egg and vanilla and beat until blended. Add the wet ingredients to the dry ingredients; stir to combine. Refrigerate the dough for 1 hour.
3. Preheat oven again to 350 degrees F. Coat two baking sheets with cooking spray. Roll tablespoons of dough into 1-inch balls and place on the prepared baking sheets about 2 inches apart. Press the tip of your index finger into the center of each cookie to make an indentation. Bake the cookies, in batches, until set and barely golden on the bottom, 13 to 15 minutes. Transfer to a wire rack; let cool for 30 minutes.
4. Cook sliced almonds in a small dry skillet over medium-low heat, stirring constantly, until lightly browned, 2 to 4 minutes. Mix remaining 1/4 cup honey and 1 Tbs. butter in a small bowl until creamy. Use 1/4 tsp. to fill each cookie and top with two sliced almonds.