Cut off the tops of each pepper. Pull out the ribs and seeds and discard. Discard the stems and dice the pepper tops. Set aside. Lightly trim the bottoms of each pepper so they can stand up.
Stand the peppers up on a baking sheet or large skillet and drizzle with oil. Season with salt and pepper then roast until they begin to soften, 5 to 8 minutes.
Heat the oil in a medium saucepot over medium-high heat. Add the garlic, jalapenos and onions and cook until the onions are translucent, 3 to 5 minutes. Add the diced pepper tops and eggplant and season with salt and pepper. Cook, stirring occasionally, until the vegetables soften and begin to caramelize, about 3 minutes. Stir in the rice and mix to combine. Add the wine and cook until it is reduced by half, 2 to 3 minutes. Add 2 cups water and the crushed tomatoes and cook, covered, stirring occasionally, until the rice is creamy and al dente, 10 to 12 minutes.
Remove the saucepot from the heat and stir in the mascarpone and basil. Taste for seasoning, adding additional salt and pepper if needed.
Reduce the oven temperature to 400 degrees F. Fill each pepper with the rice mixture, then stand them up on the same baking sheet or large skillet and top with the mozzarella. Bake until the cheese is melted and the peppers are cooked through, about 5 minutes. Serve topped with more torn basil and a drizzle of oil.