For the Tomatoes:

1. Preheat the oven to 350°F. Set out a 2 1/2-quart baking dish that is about 2 inches deep.
2. Heat the oil in a large skillet over medium-high heat. Cook the shallots, stirring occasionally until lightly browned, about 5 minutes. Add the garlic and cook until fragrant, about 1 minute. Remove from heat and transfer to a medium bowl.
3. Add the tomatoes, salt, red pepper flakes, pepper, and thyme to the bowl with the shallots. Stir together until incorporated.
4. Evenly sprinkle the flour over the tomatoes. Gently fold the flour into the tomatoes with a spatula until the flour dissolves completely into the mixture with no lumps. Set aside as you make the biscuit dough.

For the Biscuit Dough:

1. Whisk together the flour, baking powder, baking soda, and salt in a large bowl.
2. Add the cubed butter, and use a pastry cutter to incorporate it into the flour mixture until the larger lumps are reduced to pea-sized pieces.
3. Make a well in the center of the mixture and pour in 1/2 cup buttermilk. Stir with a spatula or your hands, combining everything until a thick dough forms. Do not overmix.

To Assemble and Bake:

1. Transfer and evenly distribute the tomato mixture into the baking dish.
2. Using a 1/4-cup cookie scooper, gently and evenly place 10-12 mounds of biscuit dough over the top of the tomatoes, leaving a little space between each one.
3. Lightly brush the dough with the remaining 1/4 cup buttermilk.
4. Transfer the baking dish to the oven. Bake until the tomatoes are bubbling and the biscuits are golden brown, about 50-60 minutes.
5. Transfer to a wire rack. Let cool for about 20 minutes before serving.