Heat 2 tablespoons oil in a Dutch oven over medium heat.
Add onion and three-quarters of the garlic. Cook until softened, about 4 minutes.
Stir in penne, crushed tomatoes, water, 1½ teaspoons salt, and red pepper flakes.
Bring to a boil, reduce heat, cover, and simmer until pasta is tender, about 10 minutes.
In a small bowl, combine panko, remaining tablespoon oil, remaining garlic, and a pinch of salt.
Microwave in short bursts, stirring, until golden brown, 2 to 3 minutes.
Adjust oven rack to the middle and preheat broiler.
Stir chicken into the pasta. Sprinkle mozzarella over the top.
Broil until cheese is melted and golden brown, about 5 minutes.
Top with toasted panko and serve.