Preheat oven to 425°F.
Arrange breading station: place flour on one large plate or platter. Place egg in a large mixing bowl and whisk with a fork. Place panko breadcrumbs, garlic powder, onion powder, and thyme in a separate mixing bowl or platter, and stir until well combined.
Use hands to toss diced eggplant, all in one batch, through flour until every piece is lightly coated with flour.
Transfer eggplant bites to mixing bowl containing egg. Use a large slotted spoon to carefully mix eggplant with egg, until every piece is lightly coated with egg.
Use slotted spoon to transfer diced eggplant to breadcrumb mixture. Use hands to toss eggplant through breadcrumbs until every piece is well coated.
Transfer breaded eggplant to a parchment-lined baking sheet and spread out the pieces so that no two are overlapping. Wash hands.
Season eggplant bites thoroughly with salt and pepper. Measure two tablespoons of olive oil and carefully pour over eggplant, ensuring each piece is lightly coated with oil.
Cook for about 17-20 minutes, or until eggplant bites are golden-brown and crispy.
Meanwhile, as eggplant is cooking, boil a large pot of water. Salt the water and add penne pasta. Cook about 7-8 minutes, or until just al dente, and drain.
Meanwhile, heat 1 tablespoon olive oil in a skillet over medium heat. Add onion and bell pepper and season with salt and pepper. Sauté until softened, about 5-6 minutes. Add jarred marinara, stir until well combined, and cook until heated through, about 2 minutes.
Transfer penne, veggie marinara, parmesan bites, and 2/3 cup parmesan to a large mixing bowl. Carefully stir until combined. Transfer pasta to serving bowls and top with remaining parmesan. Add chopped basil or parsley (optional), and serve.