For the tomato sauce: In a pan over medium heat, add the olive oil, onions and garlic. Sweat until soft and tender, about 10 minutes. Add the chile flakes and oregano and cook for an additional 3 minutes. Add the tomatoes, chipotle and basil sprigs and bring to a simmer. Simmer, stirring frequently, until slightly thickened, about 2 1/2 hours. Season with salt.
For the eggs: Bring 3 inches of water and the vinegar to a low simmer in a straight-sided skillet. Break each egg into a ramekin or small bowl. Gently slide each egg into the simmering water. Use a slotted spoon to gently form the egg whites into a round shape. Turn off the heat, cover and cook for 3 minutes for a soft-set yolk. Remove from the water using a slotted spoon to a paper towel-lined plate.
Preheat the oven to broil.
Transfer about 1/2 cup of the hot tomato sauce to a small cast-iron pan or ovenproof baking dish and mix with a little of the basil. Make a slight well, leaving a light covering on the bottom. Carefully transfer the poached eggs to the well. Season with a pinch of sea salt. Top with Parmesan, additional basil and a drizzle of olive oil. Broil until the sauce is bubbling and the top of the eggs are just set, about 2 minutes. Serve with grilled bread.