Arrange a rack in the upper third of the oven and preheat to 400 degrees . Invert a muffin pan and lightly grease the back side of ten muffin cups with olive oil. Pat a biscuit flat, place over a greased muffin cup and stretch the dough to cover the cup. Repeat with the remaining nine biscuits. Bake until golden-brown, 7 minutes. Let cool slightly, then remove the biscuit cups from the pan and invert onto a baking sheet to cool completely.
Meanwhile, heat a medium cast-iron skillet over medium heat. Add the 2 tablespoons olive oil, the onions and 1/4 teaspoon each salt and pepper. Cook, stirring every 3 minutes or so, until the onions are softened and browned, about 15 minutes. Divide the onion mixture among the biscuit cups.
In a small saucepan, melt the butter over medium-low heat. Whisk in the flour until smooth. Pouring slowly, whisk in the heavy cream and cook, stirring, until thickened, about 3 minutes. Remove from the heat and stir in half of the cheese; season with salt and pepper. Spoon the cheese sauce over the onions; sprinkle the the thyme and remaining cheese and on top and bake until the cheese is melted and the biscuit edges are golden, 5 to 7 minutes.