Season the short ribs with salt and pepper. Heat the oil in a large Dutch oven over high heat until shimmering. Add as many short ribs as will fit without crowding and cook, turning occasionally, until well browned on all sides, about 8 minutes per batch. Transfer to a platter and repeat with remaining ribs.
When all the ribs are browned, reduce the heat to medium and add the onion. Cook, stirring frequently, until softened, about 6 minutes. Add the chiles, garlic, and oregano and cook, stirring, until fragrant, about 1 minute. Add the chile paste and cook, stirring constantly, until the paste is sizzling and fragrant, about 2 minutes. Add the chicken stock and scrape up any browned bits from the bottom of the pot. Add the anchovies, Marmite, soy sauce, tomato paste, ground spices, cocoa, and cornmeal and whisk to combine. Keep warm over low heat.
Adjust an oven rack to the lower-middle position and preheat the oven to 225°F. Remove the meat from the bones and chop all the meat into 1/4- to 1/2-inch pieces. Add the meat, any accumulated juices, the bones, and the bay leaves to the Dutch oven. Bring to a simmer over high heat, cover, and place in the oven for 1 hour.
Meanwhile, place the soaked and drained beans in a medium saucepan and cover with water by 1 inch. Season with salt and bring to a boil over high heat. Reduce to a simmer and cook until the beans are nearly tender, about 45 minutes. Drain.
Remove the chili from the oven. Add the tomatoes, vinegar, and beans and return to the oven with the lid slightly ajar until the meat and beans are fully tender, 1 1/2 to 2 hours longer.
Remove the bay leaves and bones. Add the whiskey (if using), hot sauce, and brown sugar. Season to taste with salt, pepper, and/or vinegar.
Serve, or, for the best flavor, allow the chili to cool and refrigerate overnight, or up to 5 days in an airtight container, then reheat. Serve with some or all of the suggested garnishes and corn chips or tortillas.