Preheat oven to 400°F. Line a rimmed baking sheet with aluminum foil (for easy clean up). Place the roma tomatoes, cut side up, on the prepared baking sheet. Season well with kosher salt and freshly ground black pepper then drizzle with extra-virgin olive oil. Each tomato should be glistening with oil, not swimming in it. Place garlic cloves on a small square of aluminum foil. Sprinkle with a small pinch of kosher salt and a few turns of black pepper. Drizzle with a little extra-virgin olive oil then wrap the sides of the square around the cloves to create a tight packet. Place the packet on the baking sheet with tomatoes. Roast until the tomatoes tender and slightly caramelized (about 1 hour). Unwrap garlic and carefully peel (or squeeze). Add roasted garlic cloves, tomatoes and any juices from the baking sheet to a large, heavy bottomed pot. Pour in chicken stock. Using an immersion blender, process tomatoes and stock until a somewhat chunky consistency is achieved (some texture, but no big chunks of tomato). If you don’t have an immersion blender, I would recommend pureeing the tomatoes, garlic and juices in a food processor or blender before adding to the pot. Add thyme and red pepper flake then bring the mixture to a boil over medium heat. Reduce heat to low and cook, uncovered, for about 25 – 30 minutes, stirring occasionally. Take the soup off of the heat then season to taste with kosher salt and black pepper. While the soup is cooking, preheat oven to 350°F and line a rimmed baking sheet with aluminum foil. Place 4 – 6 ovenproof jars or bowls on the baking sheet. Stir grated onion into the soup then distribute soup evenly between your jars or bowls. Lightly butter one side of each slice of bread. Top each jar or bowl with a bread slice, buttered side up. Pile grated cheddar on top of each slice of bread. Carefully transfer the baking sheet (with soup) to your preheated oven and cook until cheese is lightly browned and bubbling (15 to 20 minutes). You can also cook the cheddar for an additional few minutes under the broiler to get the cheese extra golden. The soup is extremely hot right out of the oven, so let cool for a few moments before serving.