Combine farro and water in a small saucepan over medium heat. Cook according to package directions.
In a large soup pot or Dutch oven, heat olive oil. Add butternut squash, bell pepper, onion, and jalapeno. Cook over medium-high heat for 4 to 5 minutes or until onion is translucent. Add garlic and cook 1 minute.
Add cooked farro, tomatoes, beans, vegetable broth, oregano, cumin, coriander and cayenne. Stir in tomato paste and bring to a gentle simmer. Cover the pot and simmer for 20 minutes.
Add dark chocolate, red wine vinegar, salt and pepper to the pot. Cook another 15 minutes or until butternut squash is tender and chocolate is completely melted and incorporated into the chili.
Taste and adjust any seasonings as needed.