Preheat oven to 350F [180C]. Spray a 9-inch square baking pan with baking spray with flour. Line with parchment paper, letting excess extend over sides of pan; lightly spray parchment.
In the bowl of a stand mixer fitted with the paddle attachment, best butter, sugar, and lemon zest at medium speed until fluffy, 3 to 4 minutes, stopping to scrape sides of bowl. Add eggs, one at a time, beating well after each addition. Beat in vanilla. (Mixture may look slightly broken at this point, but batter will come together.)
In a medium bowl, whisk together flour, poppy seeds, baking powder, salt, and baking soda. In a small bowl, whisk together milk and lemon juice. (Juice will cause milk to curdle slightly, and that is okay.) With mixer on low speed, gradually add flour mixture to the butter mixture alternately with milk mixture, beginning and ending with milk mixture, beating just until combined after each addition. Spoon batter into prepared pan, smoothing into an even layer. Tap pan on your work surface several times to settle batter and release any air bubbles.
Bake until a wooden pick inserted in the center comes out clean, 30 to 40 minutes. Let cool in the pan for 10 minutes. Use the parchment sling to remove the cake from the pan, and let cool completely on a wire rack.
Pour the Crème Fraîche Glaze onto the cooled cake; using a small offset spatula, spread into an even layer. Garnish with poppy seeds and lemon zest, if desired.
For the Glaze: In a medium bowl, stir together all ingredients until smooth. Use immediately.