Cook the Pasta: Bring a large stockpot of unsalted water to a rolling boil. Add the whole-wheat rotini and cook according to package directions until perfectly al dente, typically 9-11 minutes. Immediately drain the pasta in a colander and rinse briefly under cold water to halt the cooking process. Set aside to drain completely.
Prepare the Vinaigrette: In a small jar with a tight-fitting lid, combine the extra-virgin olive oil, fresh lemon juice, lemon zest, balsamic vinegar, minced garlic, and optional red pepper flakes. Season generously with freshly ground black pepper. Seal the jar and shake vigorously for 30 seconds until the vinaigrette is creamy and fully emulsified.
Combine Ingredients: In a large mixing bowl, combine the cooled pasta, halved cherry tomatoes, sliced red onion, and torn basil leaves. Pour about two-thirds of the vinaigrette over the salad and toss gently to coat everything evenly.
Final Assembly: Gently fold in the halved mozzarella balls and the baby arugula, drizzling the remaining vinaigrette over the top. Give the salad one last gentle toss.
Serve: For the best flavor, allow the salad to rest at room temperature for 10-15 minutes. Just before serving, sprinkle the grated Pecorino Romano cheese over the top.