Preheat the oven to 400 degrees F. Line a rimmed baking sheet with foil. Toss the squash on the baking sheet with the thyme, 3 tablespoons of the oil, 1 teaspoon salt and a few grinds of pepper until the squash is well coated. Roast until very tender, about 30 minutes, stirring halfway through the cooking time.
Meanwhile, put the pistachios on a small baking sheet and toast until fragrant, about 5 minutes; set aside to cool.
Bring 4 cups of water to a boil in a medium saucepan and stir in the quinoa. Simmer, uncovered, until the quinoa is tender, about 10 minutes. Drain the quinoa and transfer to a medium bowl. Add the remaining 2 tablespoons oil, the toasted pistachios, roasted squash and vinegar, toss well and adjust the seasoning with additional salt and pepper. Sprinkle with thyme leaves. Serve warm or at room temperature.
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