Preheat your oven to 350°F (175°C), positioning a rack in the upper third of the oven for even heat distribution.

In a medium bowl, whisk together the whole wheat pastry flour, baking powder, salt, and poppy seeds until thoroughly combined. Set this aside.

In a separate large mixing bowl, cream the softened butter until it becomes light and airy, using a hand mixer or stand mixer if preferred. Add the brown sugar and continue to beat, ensuring to scrape down the sides of the bowl to maintain a smooth, uniform mixture. Incorporate the egg yolks one at a time along with the vanilla extract, mixing until just blended and scraping the bowl as necessary to integrate all ingredients evenly.

Gently fold the flour mixture into the butter mixture by hand, being careful not to overwork the dough. If the texture seems dry or crumbly, gradually stir in the milk one tablespoon at a time until the dough begins to hold together. Transfer the dough to a clean countertop and knead it gently just until it forms a cohesive mass.

Divide the dough into four equal portions. Shape each into a ball, then flatten each into a disk roughly 1/2-inch thick. Wrap each disk tightly in plastic wrap and refrigerate for a minimum of 30 minutes to allow the dough to firm up and become easier to roll out.

Once chilled, roll the dough out on a lightly floured surface to a very thin sheet—about 1/8-inch thick. Use your favorite cookie cutter to stamp out shapes, gathering and re-rolling scraps as needed. Arrange the cookies about 1 inch apart on a parchment-lined baking sheet. If desired, sprinkle the tops lightly with flaky sea salt and turbinado sugar for added texture and flavor.

Bake the cookies for about 7 minutes, or until the edges take on a light golden hue. Remove from the oven and transfer the cookies to a wire rack to cool completely.

When ready to assemble, melt the dark chocolate in a double boiler or a heatproof bowl set over a pot of gently simmering water, stirring occasionally until smooth. Place about 1/2 teaspoon of melted chocolate on the flat side of one cookie, then sandwich with another cookie, pressing lightly to spread the chocolate to the edges. Repeat with the remaining cookies and allow them to set at room temperature until the chocolate firms.