Warm the skillet over medium heat and add 2 tablespoons of the olive oil. Sauté the onions until translucent, about 5 minutes. Add the garlic and sauté for another 2 minutes. Remove from heat.
Lightly brush the bottom of the baking dish with olive oil. Arrange zucchini slices around the bottom of the pan, then add a layer of tomatoes. Sprinkle on the chopped parsley. Repeat with another layer of zucchini and another layer of tomatoes, then sprinkle on the basil chiffonade. Add the final layer of zucchini, then the tomatoes.
Arrange the onions and garlic around the top of the casserole. Sprinkle on a pinch or two of sea salt and a few grinds of black pepper. Drizzle the remaining olive oil around the top and sprinkle on the Parmesan cheese.
Bake in the preheated oven for 45 to 60 minutes. At the 45 minute mark the zucchini will be tender but not soft, so bake longer if you want it very tender. Remove from the oven and allow to rest about 5 minutes before serving. There will be plenty of juice in the bottom of the pan, and you can drizzle it over the top for more flavor.