Place the barley and water in a small saucepan with a healthy pinch of salt. Place the saucepan over high heat and bring the water to a boil. Reduce to a simmer and cover. Let cook for 35 minutes or until most of the water has been absorbed and the grains are tender. You may have to drain away some excess water. Transfer the barley to a bowl and set aside.
While the barley is cooking, preheat the oven to 425°F.
Place the rapini in a large bowl and set aside. Mince the garlic and add 1 clove of it to the bowl with the rapini. Next, add half of the olive oil, half of the crushed red pepper flakes and half of the salt. Toss to coat and transfer the rapini to a large baking sheet lined with parchment paper. Set aside.
Add the buttercup squash to the now empty bowl. Add the remaining olive oil, salt, crushed red pepper flakes, and garlic. Toss to coat. Arrange the wedges on another baking sheet lined with parchment paper.
Place the squash in the oven and roast for 15 minutes. Remove the squash and flip the wedges. Return the squash to the oven and add the rapini. Roast for an additional 15 minutes. Remove the veggies from the oven and set aside.
While the veggies are roasting, take 3/4 cup of the pumpkin seed pesto and add it to the pearl barley. Stir the pesto into the barley until it is evenly coated. Add half of the bocconcini and toss to disperse.
Transfer the dressed barley to a large serving platter and top with roasted squash wedges, roasted rapini, the remaining bocconcini and a sprinkling of pepitas. Serve immediately.