Bring a large pot of salted water to a boil. Heat 3 tablespoons olive oil in a large wide pot or Dutch oven over medium-high heat. Add the garlic and cook, stirring occasionally, until golden brown, 2 to 3 minutes. Stir in the red pepper flakes, then add the tomatoes and 1/2 teaspoon salt. Bring to a steady simmer and cook until thickened, 7 to 10 minutes.
Meanwhile, add the pasta to the boiling water and cook as the label directs for al dente. Reserve 1 cup cooking water, then drain.
During the last 4 minutes of cooking the pasta, add the wine and scallops to the tomato sauce, stirring to evenly distribute the scallops in the sauce. Simmer until just cooked through, about 4 minutes.
Add the pasta and 1/2 cup cooking water to the scallops. Cook, stirring, until the pasta is well coated, 1 to 2 minutes. Add some of the remaining cooking water, a few tablespoons at a time, if the pasta is dry; season with salt. Stir in 3 cups arugula to wilt slightly.
Divide the pasta among shallow bowls. Top with the remaining 1 cup arugula and drizzle with the remaining 2 tablespoons olive oil. Finely grate the lemon zest over the pasta and top with more red pepper flakes.