Preheat the oven to 375ºF. Line a baking tray with parchment. Carefully core the peppers by cutting around the stem and pulling it out. Slice the peppers in half lengthwise and remove the pith and remaining seeds. Place the peppers cut-side down on the baking sheet. Pour about ⅓ of a cup of water onto the tray and place it in the oven. Bake for about 25 minutes or until the peppers are soft but still hold their shape.
In a large pan, heat oil over medium heat. Add onions, garlic, and salt. Cook, stirring occasionally until the onions are soft, 5 to 8 minutes. Add the chili powder, cumin, and chipotle. Cook for a minute or two until spices are fragrant. Add the jackfruit and beans. Stir and cook for a few minutes until the flavors have combined. Stir in the BBQ sauce and cook for another 5 minutes. Squeeze in lime juice, stir, and set aside.
To make the polenta, bring water, salt, garlic and onion powders to a gentle boil. Whisk in polenta, and cook while stirring continuously for another 3 to 5 minutes, depending on package instructions. The polenta should be loose and spoonable, not firm. Remove from heat.
Arrange peppers in a baking dish that’s small enough that the peppers touch each other: this will help provide support when you add the filling. Spoon several tablespoons of polenta into each pepper, followed by several spoonfuls of jackfruit and bean mixture. Top with shredded vegan cheese, if desired. Bake for 10 to 15 minutes to ensure everything is evenly heated. Serve immediately, topped with avocado and tomato, if you like.