Place rack in center of oven; preheat oven to 350°F.
Place 2 Tbsp. unsalted butter in a 2–3-qt. shallow baking dish or medium (10") ovenproof skillet. Transfer to preheating oven and heat until butter has melted, about 4–6 minutes.
Meanwhile, blend 3 large eggs, 1 cup whole milk, ⅓ cup granulated sugar, 1 tsp. vanilla extract, 1 tsp. finely grated lemon zest, and 1 tsp. kosher salt in a blender on medium speed until frothy, about 2 minutes.
Add ½ cup all-purpose flour and blend on low speed just until combined.
Pour batter into hot baking dish. Working quickly, arrange 2 cups prepared fruit evenly over and sprinkle with the remaining 2 Tbsp. granulated sugar.
Bake clafoutis until top is puffed and lightly golden brown, 25–35 minutes.
Let cool slightly, then sift powdered sugar over (if using). Serve warm or room temperature.