Melt 2 Tbsp. butter in a large, heavy skillet over low heat. Add onions, 1/2 tsp. salt and thyme; cook until tender and lightly browned, 30 minutes. Set aside to cool.
Place one rack in upper third of oven and another in lower third; preheat oven to 400°F. Coat 2 baking sheets with cooking spray.
Mix flour, baking powder, sugar and remaining 1/2 tsp. salt in a bowl. Cut remaining 6 Tbsp. butter into small chunks and add to flour mixture. Cut in butter using your fingers, 2 knives or a pastry blender until mixture resembles coarse meal. Stir in milk with a fork just until flour is evenly moistened.
Turn out dough onto a floured surface and pull together into one piece with floured hands. Divide dough into 48 mounds (about 1/2 Tbsp. each); roll each into a ball and place on baking sheets. With a teaspoon measuring spoon, press an indentation into center of each ball. Spoon onion mixture into indentations.
Bake, rotating pans halfway through, until golden, 12 to 15 minutes. Serve warm.