Prep the Oven and Pan: Preheat your oven to 400°F (200°C).
Build the Base: In the bottom of a large ceramic baking dish, stir together the marinara sauce (or tomato passata), minced garlic, and 1 tablespoon of olive oil until smooth and flat.
Shingle the Vegetables: Alternately shingle the zucchini rounds and tomato slices in tight, overlapping rows across the entire pan on top of the sauce layer.
Season: Drizzle the remaining 1 tablespoon of olive oil over the vegetables. Season evenly with dried Italian seasoning, sea salt, and cracked black pepper.
Add Cheese and Bake: Scatter the shredded mozzarella and grated Parmesan cheese evenly over the top. Bake uncovered for 25 to 30 minutes until the vegetables are tender and the cheese is melted and bubbling.
Broil: Turn the oven to broil and cook for 2 minutes, watching closely until the cheese is spotty golden-brown.
Garnish and Serve: Remove from the oven, garnish with fresh thyme sprigs, and let rest for 5 to 10 minutes before serving.