Preheat oven to 350°F. Cut a little bit off the end of each squash half, if needed, to help it stand cut side up. Lightly coat squash with 1 tbsp oil, sprinkle with pinch each salt and pepper and place cut side down on a large baking sheet. Bake for 40 minutes.
Meanwhile, cook quinoa: In a small saucepan, bring quinoa and 3/4 cup water to a boil. Reduce heat to low, cover and simmer for 10 minutes. Remove from heat; fluff with a fork.
Meanwhile, in a small skillet on medium, heat 1 tbsp oil. Add onion and cook until softened and starting to turn golden, 4 to 6 minutes.
In a large bowl, whisk together remaining 2 tbsp oil, vinegar, honey, lime juice, mustard, cayenne pepper (if using), and remaining pinch each salt and pepper. Add quinoa, onion, spinach, cranberries and walnuts; toss to coat.
To each squash cavity, place one-quarter of quinoa mixture in each well, pressing to fit.
To heat, place one serving on baking sheet and cook for 15 minutes at 350°F or until squash is soft and filling is hot. To heat leftovers directly from refrigerator, heat at 350°F for 30 minutes.