Preheat oven to 400F. Cut zucchini in half lengthwise and scoop out the flesh with a spoon, leaving a 1/4-inch thick shell. Reserve 1 cup of the scooped flesh, finely chop it, and set aside. Brush the cut sides of the zucchini shells with olive oil and sprinkle with salt. Place cut-side down on a baking sheet and roast for 12 minutes until just tender but still holding shape.

While zucchini roasts, combine quinoa and vegetable broth in a medium saucepan. Bring to a boil, then reduce heat to low, cover, and simmer for 15 minutes until liquid is absorbed and quinoa is fluffy. Remove from heat and let stand covered for 5 minutes, then fluff with a fork.

Heat 1 tablespoon olive oil in a large skillet over medium heat. Add onion and cook for 5 minutes until softened and translucent. Add garlic and the reserved chopped zucchini flesh; cook 3 minutes more until the moisture evaporates and mixture begins to brown lightly.

Remove skillet from heat. Stir in the cooked quinoa, sun-dried tomatoes, basil, oregano, half the mozzarella, Parmesan, and red pepper flakes if using. Taste and season with salt and pepper - the filling should be highly seasoned since the zucchini is mild.

Flip the par-cooked zucchini shells cut-side up. Mound the filling generously into each shell, pressing lightly to pack. Top with remaining mozzarella. Return to the oven and bake 15-18 minutes until the cheese is melted and bubbling with light golden spots. Let rest 5 minutes before serving, garnished with fresh basil.