Preheat the oven to 425 degrees . Drizzle the flesh of the squash with olive oil and season with salt, pepper and the nutmeg. Place the squash, cut side down, in a large baking pan and pierce the skin in several places with a fork. Bake for 45 minutes. Turn the squash over and bake until the spaghetti-like strands can be easily removed with a fork, about 10 minutes more. Let cool before scraping the flesh into a bowl.
Arrange 2 racks in the upper and lower thirds of the oven and preheat to 475 degrees . Sprinkle 2 large, heavy baking sheets with the cornmeal. Place the pizza dough rounds on top of the cornmeal and shape into 12-by-14-inch rectangles. Brush with olive oil and sprinkle with salt and the chopped thyme. Bake until golden and crisp, 15 to 20 minutes.
Spread the ricotta evenly over the pizza crusts and top with the squash. Season with thyme leaves, salt and pepper, then drizzle with olive oil. Bake until just warmed through, about 5 minutes. Cut the pizza into squares and serve with the lemon wedges.