Combine both flours, baking soda, salt, and yogurt in a large bowl. Mix thoroughly to break up any lumps, then make a well in the center and add the water and eggs. Whisk to a smooth, uniform batter and set aside to rest while you prepare the topping.

Heat three tablespoons of oil in a frying pan over medium heat. Add the red onions and cook for 12 to 15 minutes, stirring occasionally, until they have caramelized and turned a deep golden brown.

Stir in the green chiles, salt, and black pepper. Add the sliced tomatoes, stir to combine, then immediately remove from the heat so the tomatoes hold their shape.

Place a non-stick frying pan over medium heat and add a teaspoon of oil. Once hot, pour a small ladleful of batter into the pan and smooth it out into a 4-inch round with the back of the ladle.

Allow the batter to set for 1 minute, then place a generous tablespoon of the tomato-onion mixture on top. Flip the uttapam and cook for another minute until the pancake is cooked through and the vegetables are slightly charred.

Transfer to a plate and repeat with the remaining batter and topping. Serve warm with a side of sambhar and coconut chutney.