Tip:To adapt a slow-cooker recipe to a conventional oven, follow these guidelines: add more liquid, to accommodate for greater evaporation; bring the dish to a boil over high heat in a Dutch oven, then cover the pot and put in a 350°F oven. Plan on the dish taking roughly half the time to cook in the oven as it would in the slow cooker.
Heat half of the oil in a 10-inch, heavy sauté pan over medium-high heat. When warm, add the bell peppers, scallions, garlic, jalapeño, half of the salt, the black pepper, and chili powder, and sauté until the vegetables are softened, about 6 minutes. Add the squash and sauté until slightly softened, another 3 minutes. Transfer to the slow cooker, add the beans, and mix well.
Reduce the heat to medium under the sauté pan and add the remaining oil, plus the tomato paste, chiles or chipotle liquid, and flour. Cook until the mixture is thickened and the flour disappears, about 1 minute. Increase the heat to high and add the tomatoes with their juices, the stock, lime juice, and remaining salt. Boil, stirring well, for 2 minutes, and pour into the slow cooker. Cover and cook on low to meld the flavors, 3 to 4 hours. Stir in the cilantro, and serve with the chips, avocado, and sour cream, if desired.