Preheat your oven to 400°F (200°C) and lightly grease a 9x13-inch baking dish.
Place the sliced zucchini and yellow squash in a colander, toss with 0.5 tsp kosher salt, and let them rest for 20 minutes to release excess moisture. Pat dry with paper towels.
Heat 1 tbsp olive oil in a large skillet over medium heat. Add the sliced onions and cook for 10 minutes until softened and lightly caramelized. Stir in the minced garlic and cook for 1 additional minute.
Spread the cooked onion and garlic mixture evenly across the bottom of the prepared baking dish.
Arrange the zucchini, yellow squash, and tomato slices in overlapping rows on top of the onion mixture. Drizzle with the remaining 1 tbsp olive oil and season with the remaining 0.5 tsp kosher salt, black pepper, and 1 tbsp fresh thyme.
In a small bowl, combine the panko breadcrumbs, grated Parmesan cheese, and remaining 1 tbsp fresh thyme.
Cover the baking dish with aluminum foil and bake for 30 minutes.
Remove the foil, sprinkle the breadcrumb and cheese mixture evenly over the vegetables, and bake uncovered for an additional 15 minutes until the topping is golden brown and the vegetables are tender.
Remove the baking dish from the oven and let it rest for 10 minutes before serving.