Preheat oven to 400 degrees. In a large nonstick skillet, heat oil over medium. Add bell peppers and onion and cook, stirring, until softened, 8 to 10 minutes. Add garlic and cook until fragrant, 1 minute. Stir in tomatoes and cook 3 minutes. Stir in spinach and pinch of red-pepper flakes, if using. Season with salt and pepper.
Transfer sauce to four 14-ounce gratin dishes or a 2-quart shallow baking dish. With the back of a large spoon, make 4 wells in sauce and crack 2 eggs into each. Bake until whites are set but yolks are still runny, about 25 minutes, rotating dishes halfway through. To serve, top with goat cheese and cilantro.
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