Pulse tomatoes and liquid in a food processor until chopped. Heat oil and red pepper flakes in a saucepan over medium heat. Add garlic and onion. Cook, stirring, until onions are tender, about 6 minutes. Add tomatoes and stock and bring to a boil. Reduce to a simmer and stir occasionally, until slightly reduced, about 30 minutes. Puree until smooth; season with salt and pepper.
Meanwhile, drizzle bread with oil. Toast in 375 degrees oven until it begins to turn golden, about 5 minutes. Top with mozzarella and return to oven. Cook until cheese begins to melt, about 1 minute more.
Top with fresh basil, season with salt and pepper, and serve with soup.