Preheat oven to 325 degrees. Heat 1 teaspoon olive oil in a large skillet set over medium heat. Add green zucchini, half the scallions, half the garlic, A teaspoon marjoram, 1/2 teaspoon salt, and 1/4 teaspoon pepper; cook, stirring frequently, until zucchini has softened and is beginning to brown, about 5 minutes. Remove from heat; transfer to a large bowl; set aside.
Rinse skillet; repeat process with yellow zucchini and remaining teaspoon olive oil, scallions, garlic, 1/2 teaspoon marjoram, 1/2 teaspoon salt, and 1/4 teaspoon pepper. Transfer to bowl with cooked green zucchini; let sit until cooled. Drain and discard any liquid.
Add dill, parsley, and eggs to zucchini; stir to combine. Pour into a 9 1/2-inch round, deep baking dish. Cover with tomato; sprinkle with feta. Bake until set, about 1 hour. Serve hot or at room temperature.