Butternut Squash, Zucchini and Tomato Gratin

unsalted butter

large yellow onions, thinly sliced

½ tsp dried thyme

medium butternut squash, quartered lengthwise, peeled and cut into ¼-inch thick slices

zucchini, cut into ¼-inch thick slices

tomatoes, cut into ¼-inch thick slices

½ tsp Celtic sea salt

½ cup grated Pecorino Romano cheese