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.