Make the filling: Heat oil in a large high-sided skillet over medium heat. Cook onions, stirring occasionally, until caramelized, about 25 minutes. Add garlic, and cook until fragrant, about 3 minutes. Let cool.
Toss onion mixture, tomatoes, flour, and red-pepper flakes with 1 1/2 teaspoons salt and some pepper.
Preheat oven to 375 degrees. Make the biscuit topping: Whisk together flour, baking powder, and 1 teaspoon salt in a bowl. Cut in butter with a pastry cutter or rub in with your fingers until small clumps form. Stir in cheese, then add cream, stirring with a fork to combine until dough forms. (Dough will be slightly sticky.)
Transfer tomato mixture to
a 2-quart baking dish (2 inches deep). Spoon 7 clumps of biscuit dough (about 1/2 cup each) over top in a circle, leaving center open. Brush dough with cream, and sprinkle with remaining tablespoon cheese. Bake until tomatoes are bubbling in the center and biscuits are golden brown, about 1 hour 10 minutes. Transfer to a wire rack. Let cool for 20 minutes.