Arrange the eggplant halves cut-side up on a rimmed baking sheet. Using the tip of a knife, score the flesh of the eggplant, being careful not to cut all the way through. Rub them evenly with 2 tablespoons olive oil and season with the salt. Roast until tender, 15 to 20 minutes.
Remove the eggplant from the oven and divide the marinara evenly over the halves. Sprinkle with the mozzarella. Mix together the breadcrumbs, Parmesan and remaining 2 tablespoons olive oil in a small bowl. Top the eggplant with the breadcrumb mixture and return to the oven until golden brown and bubbly, about 12 minutes. Sprinkle with the basil and pepper flakes.