Preheat the oven to 400 degrees. Line a large baking sheet with aluminum foil.
Rub the cut sides of the squash with 1 tsp. oil; season with salt and pepper. Place the squash, cut side down, on the baking sheet. Roast until the squash is tender when pierced with a fork, 25 to 30 minutes. Reduce the oven temperature to 350 degrees.
Meanwhile, in a medium nonstick skillet, heat 1 tbsp. oil over medium. Add the onion and cook, stirring occasionally, until golden, about 9 minutes. Stir in the raisins; cook until the flavors meld, about 3 minutes more. Transfer to a medium bowl.
In a small saucepan with a lid, bring 1 cup water and 1/4 tsp. salt to a boil. Stir in the couscous. Cover; remove from the heat. Let stand 5 minutes; fluff with a fork and transfer to the bowl with the onion mixture. Turn the squash halves over; scoop out 3 tbsp. of flesh from each half; mix into the couscous mixture along with 1 tbsp. oil, 1 tbsp. balsamic vinegar and the capers; season.
Divide the filling among the squash halves, then transfer the squash to the baking sheet. Bake until the filling is heated through, 10 to 12 minutes.
In a large bowl, toss the spinach, beans, cheese, remaining 1 tbsp. oil and remaining 2 tsp. balsamic vinegar; season. Serve the salad with the squash.