Preheat the oven to 400° F.In a 9×13 inch baking dish, combine the zucchini, olive oil, garlic, shallots, thyme, Italian seasoning, chili flakes, salt, and pepper. Roast 15 minutes. Pull the zucchini out of the oven. To the same pan, add the corn, orzo, and pesto. Pour over 2 1/2 cups of water and stir to combine. Return the dish to the oven and bake for 12-15 minutes, until most of the water has cooked into the pasta, but not all of it.Stir the pasta around, then sprinkle over the cheeses. Bake another 10 minutes, until the cheese has melted and the sauce is bubbling. If there's a lot of oil from the pesto on top, drain off the excess. Top with fresh basil!