Heat the oven to 400ºF. Sprinkle the cut sides of the squash with ¼ teaspoon of the salt and ⅛ teaspoon of the pepper. Place the squash (cut sides down) on a large rimmed baking sheet or roasting pan. Put the pan in the oven and pour ¼ inch of hot tap water into the pan. Roast the squash until it is almost tender, 30 to 35 minutes. Remove it to a work surface and carefully discard the hot water from the pan.
Meanwhile, rinse the quinoa in a mesh strainer under running water until the water runs clear, 1 minute.
Toast the pine nuts in a dry medium saucepan over medium heat for about 5 minutes, shaking the pan now and then. Remove the nuts from the pan and set them aside. Add the oil to the pan and when it is hot, add the onion and bell pepper and cook until tender, 5 minutes. Add the garlic and cook for 1 minute. Stir in the rinsed quinoa, chipotle peppers, paprika, cilantro, toasted pine nuts, and remaining ¾ teaspoon of salt and ⅛ teaspoon of pepper. Cook for 1 minute; then stir in the broth and bring it to a boil over high heat. Reduce the heat to low, cover the pan, and simmer the quinoa until it is tender and the liquid is absorbed, 15 to 20 minutes.
Set the squash (cut sides up) on the baking sheet and fill the hollows with the quinoa mixture. Place the stuffed squash in the oven and roast at 400ºF until it is tender and the tops are lightly browned, about 15 minutes.
Tip: You can cook the squash and quinoa ahead of time and refrigerate them for up to two days. Then just stuff the squash and roast it as directed, adding five minutes to the final cooking time.