Place an oven rack in the centre position and preheat to 425°F (220°C).
In a large Dutch oven or braiser, heat the olive oil over medium heat. Add the onion and cook, stirring occasionally, until soft and golden brown around the edges, 8 to 10 minutes. Add the garlic, chipotle peppers and adobo sauce, and cumin and cook, stirring frequently, until fragrant, 1 to 2 minutes. Pour in the passata. Use the water to rinse the jar and pour the contents into the pot. Add the fire-roasted tomatoes and tamari, stir, and bring to a simmer over medium heat. Stir in the quinoa.
Cover the pot with a lid and bake for 20 minutes, or until the quinoa is fully cooked.
Remove the chipotle-quinoa from the oven and reposition the rack, if needed, so that the top of the pot is 4 to 5 inches (10 to 12 cm) under the broiler. Set the oven to broil.
To the pot, stir in the pinto beans, corn, 1 cup of the cheddar, and cilantro. Sprinkle with the remaining 1 cup cheddar. Broil until the cheese is golden brown and bubbling, 4 to 8 minutes. (Watch carefully, as broil times vary.) Remove from the oven and top with pickled red onions, scallions, and more cilantro.