In a large ovenproof skillet, heat olive oil over medium heat. Add onions and saute for 10 minutes, stirring occasionally until golden brown and fragrant. Turn heat to medium-low. Add garlic, stirring more frequently until it becomes golden brown. About 2 minutes.
Add diced tomatoes, lemon zest and lemon juice, salt, pepper and spices. Simmer until tomatoes cook down somewhat, about 5 minutes. This will seem like a fairly “dry” tomato sauce, but the zucchini will release its liquid while baking.
Remove 2/3 of the tomato sauce and place in a separate bowl. Spread the remaining tomato sauce evenly on the bottom of the pan. Place one single layer of zucchini and summer squash in skillet slightly overlapping each disk.
Sprinkle with a generous pinch of kosher salt and pepper.
Spread remaining sauce over the zucchini and summer squash, as evenly as possible.
Add the second and final layer of slightly overlapping zucchini and summer squash. Sprinkle with salt, pepper, and the rest of the tomato sauce.
Cover with foil. Place in 350 degree oven for 40 minutes. Uncover and give a good shake, and bake uncovered for an additional 15 minutes. Let stand 10 minutes before serving. Sprinkle with parsley and a give a good drizzle of olive oil.