Preheat the oven to 400 degrees F.
Halve the bell peppers lengthwise and remove the seeds. Season with salt and pepper and drizzle with EVOO. Place the peppers cut-side down in a large casserole dish. Cut an X in the hull of each pepper and roast for 20 minutes. Let cool slightly.
Meanwhile, in a mixing bowl, grate the tomatoes on the large holes of a box grater, discarding the skins. (You should have about 2 cups.) Grate the garlic, chile pepper and onion into the bowl and season with salt and pepper. Add a drizzle of EVOO and the thyme.
Heat the butter and 1 tablespoon EVOO in a medium saucepan over medium heat. Add the orzo and toast until golden and fragrant. Add half the tomato sauce and the rice and stir for 1 to 2 minutes. Add the stock and bring to boil. Reduce the heat to a simmer, cover and cook until the rice is tender, 17 to 18 minutes.
Combine the rice mixture, meatballs and 3/4 cup Parmigiano-Reggiano. Spoon the filling into the peppers and top with the remaining tomato sauce, the remaining cheese and a drizzle of EVOO. Bake until heated through and the tops are browned, about 45 minutes.
Cook's Note: The stuffed peppers can be covered and refrigerated for a make-ahead meal. Bring to room temperature before baking.