1. Rinse the blueberries and drain them on paper towels.
2. Place a rack in the center of the oven and preheat the oven to 350°F. Lightly mist only the sides of two 9-inch round pans with vegetable oil spray, then dust them with flour. Shake out the excess flour.
3. Using a pencil, trace the bottom of a 9-inch round pan onto two pieces of parchment paper. Cut out the two round pieces of paper, place them in the bottom of the two prepared cake pans, and set them aside.
4. Place the flour and brown sugar in a medium-size bowl and toss with your fingers until well mixed. Cut the butter into small cubes and add it to the flour and brown sugar mixture. Using a pastry blender or 2 knives, cut the butter into the mixture until it resembles coarse crumbs. Add the pecans to the mixture and toss to combine. Evenly sprinkle this topping mix onto the parchment paper rounds, about ¾ cup in each cake pan. Set the pans aside.
5. Rinse the lemon and pat it dry with paper towels. Grate 1 teaspoon of lemon zest. Cut the lemon in half and squeeze the juice into a small bowl; you will have about 2 tablespoons. Set 1 tablespoon of juice aside for the glaze.
6. Measure out 1 tablespoon of the cake mix and set it aside. Place the remaining cake mix and the yogurt, water, oil, eggs, and the remaining 1 tablespoon of lemon juice, and the lemon zest, in a large mixing bowl. Beat with an electric mixer on low speed until the ingredients are incorporated, 1 minute. Stop the machine and scrape down the side of the bowl with a rubber spatula. Increase the mixer speed to medium and beat for 2 minutes longer, scraping down the side of the bowl again if needed. The batter should look well blended.
7. Set aside 1/4 cup of the drained blueberries for garnish. Place the remaining blueberries in a small bowl and toss them with the reserved 1 tablespoon of cake mix. Fold the blue-berries into the cake batter until just evenly combined. Using a large mixing spoon, dollop the cake batter on top of the topping in each cake pan, then carefully spread it evenly to the edges. Place the cake pans in the oven side by side.
8. Bake the cake layers until they are golden brown and the tops spring back when lightly pressed with a finger, 24 to 28 minutes. Transfer the cake pans to wire racks and let the cake layers cool for 5 minutes. Run a long, sharp knife around the edge of each cake layer and give the pans a good shake to loosen the cakes. Invert each layer onto a wire rack so that the topping side is up. Let the layers cool to room temperature, 20 minutes longer, if desired. Peel off and discard the parchment paper circles.
9. For the glaze, whisk the confectioners' sugar and reserved 1 tablespoon of lemon juice in a small bowl. Add 1 tablespoon of milk at a time until the glaze is smooth but still runny enough that it will slowly drip down the side of the cake.
10. To assemble the cake, transfer one layer, topping side up, to a serving platter. Using a spoon, drizzle half of the glaze over the cake and allow it to drip over the edge. Place the second layer on top of the first and drizzle the remaining glaze over it. Garnish the top of the cake with the reserved ¼ cup of blueberries.