Preheat the oven to 375° F with a rack in the center position. Line a large baking dish with parchment paper or aluminum foil.
Using a small spoon, scoop out the flesh of the zucchini, leaving a ⅓-inch thickness around the edges. Place them cut side up in the prepared baking dish.
Heat the olive oil in a large skillet set over medium-high heat. Once the oil is glistening, add the chicken, bell pepper, and garlic. Cook, breaking the meat up with a wooden spoon until it’s cooked through and there is no longer any liquid in the skillet, about 10 minutes.
Stir in 2¼ cups of the marinara sauce. Bring to a simmer and cook, stirring occasionally until slightly thickened, about 10 minutes.
Meanwhile, in a medium bowl, combine the ricotta cheese, spinach, garlic powder, egg, 1 tablespoon of parsley, salt, and pepper.
Fill each zucchini boat with equal amounts of the chicken mixture. Dollop the ricotta mixture on top of the chicken. Sprinkle all over with half of the mozzarella. Pour the remaining marinara over the zucchini boats and sprinkle with 2 tablespoons of Parmesan cheese. Cover the baking dish with aluminum foil.
Bake for 20 minutes. Remove the baking dish from the oven. Discard the foil. Sprinkle with the remaining 1 cup mozzarella. Return the dish to the oven and bake until the cheese is lightly browned and melted and zucchini is tender, about 15 minutes more.
Serve warm, sprinkled with the remaining 2 tablespoons Parmesan, remaining 1 tablespoon parsley and red pepper flakes if using.
