Preheat oven to 425°F. Trim squash ends and cut the squash crosswise into 4 equal rounds. Scoop out and discard the seeds. Place the rounds on a rimmed baking sheet. Drizzle with 2 tablespoons oil and sprinkle with ¼ teaspoon pepper. Roast until the squash is tender, 30 to 40 minutes.
Meanwhile, heat the remaining 1 tablespoon oil in a large skillet over medium-high heat until shimmering. Add chopped onion; cook, stirring occasionally, until softened, about 4 minutes. Stir in rinsed beans, chopped spinach, 1½ tablespoons vinegar, 1½ teaspoons garlic powder, ¼ teaspoon crushed red pepper, ¼ teaspoon salt and the remaining ¼ teaspoon pepper. Cook, stirring, until the spinach is just starting to wilt, 1 to 2 minutes. Remove from heat and fold in half of the ¾ cup feta.
Using a fork, shred the squash in the center of the rings into long strands. Divide the spinach mixture among the squash nests. Sprinkle evenly with the remaining feta. Bake until the feta is slightly melted and the filling is warmed through, about 5 minutes. Top with 2 tablespoons basil.
