Slice your summer squash into uniform 1/4-inch rounds. Toss the sliced squash with 1 teaspoon of salt in a colander and let sit for 15 minutes to draw out excess moisture.
In a large skillet, heat olive oil over medium heat. Add onions and cook until translucent, about 5 minutes. Add garlic and thyme, cooking for another minute until fragrant.
Preheat your oven to 375°F (190°C). Pat the squash dry with paper towels. In a 9x13-inch baking dish, arrange half of the squash in overlapping layers. Season with pepper and sprinkle with 1/3 of the cheese mixture.
Add the onion mixture as the next layer.
Add remaining squash in an attractive pattern (concentric circles work beautifully) and pour the cream evenly over the top.
Mix the remaining cheeses with panko breadcrumbs and melted butter. Sprinkle this mixture evenly over the top of the gratin.
Bake uncovered for 35-40 minutes until the top is golden brown and the casserole is bubbling around the edges. Let stand for 10 minutes before serving.