Line a baking sheet with parchment paper. Spread the onions, tomatoes, and gnocchi on the sheet pan.
In a small bowl, whisk together the oil, prepared pesto, salt, dried basil, dried oregano, and red pepper flakes. Drizzle the pesto mixture over the gnocchi and veggies and toss to combine, ensuring the gnocchi are all coated.
Spread the onions, tomatoes, and gnocchi in an even layer, then transfer to the oven and bake for 22 minutes, shaking the pan halfway through to evenly roast the gnocchi.
Remove from the oven, toss the gnocchi once more, and crumble the goat cheese over top. Bake for 2 more minutes.
Turn the broiler on high and broil for 2 to 3 minutes or until the cheese is bubbly and the gnocchi is crisp. Remove from the oven and dollop the remaining pesto over the top.
To serve, add a small handful of arugula to each bowl. Arrange the gnocchi over the greens. Garnish with lemon zest, shaved Parmesan cheese, pine nuts, and red pepper flakes.