Place 1/4 cup all-purpose flour, 1/2 teaspoon garlic powder, and 1/2 teaspoon onion powder in a shallow bowl or plate and whisk to combine. Place 1/2 cup panko breadcrumbs and 2 ounces Parmesan cheese to a second shallow bowl or plate and whisk to combine. Add 2 large eggs to a third shallow bowl or plate and whisk to combine.
Slice 2 boneless, skinless chicken breasts in half horizontally (also known as butterflying). Season all over with 3/4 teaspoon kosher salt and 1/4 teaspoon black pepper.
Working with one piece of chicken at a time, coat the chicken in the flour mixture, then dip in the egg, letting any excess drip off. Coat in the panko-Parmesan crumbs. Place on a baking sheet or plate in a single layer.
Heat an air fryer to 400°F. Place 2 breaded chicken pieces in a single layer in the air fryer basket, making sure they do not overlap. Coat with cooking spray. Air fry until golden and crisp, 5 to 6 minutes.
Top each piece of chicken with a slice of mozzarella cheese, and secure each piece of cheese with 2 toothpicks. Air fry until the chicken is golden brown, an instant-read thermometer inserted into the center registers at least 165°F, and the cheese melts, 1 to 2 minutes more.
Transfer to a plate and cover loosely with aluminum foil. Repeat air frying the remaining chicken and cheese. When the second batch is almost ready, warm 1 cup marinara sauce on the stovetop over medium heat or in the microwave until warm.
To serve, remove the toothpicks, divide the marinara sauce evenly among serving plates, and nestle each serving of chicken Parmesan on top. Garnish with fresh basil leaves, if desired.