Heat the oven to 325°F with a rack in the lower-middle position. Pulse the mushrooms in a food processor about 10 times until they are coarsely chopped and uniform in size.

Toast the mustard seeds and cumin seeds in a Dutch oven over medium heat, stirring constantly, until fragrant, about 1 minute. Stir in the oil, onion, and processed mushrooms, cover, and cook until the vegetables have released their liquid, about 5 minutes.

Uncover the pot and continue to cook until the liquid has evaporated and the vegetables are browned, 5 to 10 minutes.

Stir in the garlic and chipotle and cook until fragrant. Add the chili powder and cook, stirring constantly, for about 1 minute to develop the flavor.

Stir in the broth, water, beans, sugar, baking soda, and bay leaves; bring to a simmer over medium-high heat, skimming any foam that rises to the surface.

Cover the pot and transfer it to the oven to cook for 1 hour.

Stir in the crushed tomatoes and bell peppers, then return the pot to the oven, covered, until the beans are fully tender, about 1 hour more. If the chili begins to stick or looks too thick, stir in a little extra water as needed.

Discard the bay leaves and stir in the cilantro. Season with salt and pepper to taste and serve hot.