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Heat oven to 350 degrees. Make the spice blend: In a small bowl, combine brown sugar, thyme, smoked paprika, garlic powder, mustard powder, cayenne pepper, 1 teaspoon kosher salt such as Diamond Crystal (or ¾ teaspoon fine salt), ¼ teaspoon black pepper and lemon zest, if using.
Slice onions crosswise into ¼-inch-thick rings. (Cut them very thinly, so you end up with silky onions, not crunchy ones.) Transfer them to a bowl, separating the rings into individual pieces. Gently toss with olive oil, the spice blend and the juice from one half of the lemon, if using, until coated.
Arrange half of the onions in the bottom of a 3-quart or 9-by-13-inch baking dish. Sprinkle with half of the Cheddar and half of the Swiss. Layer the remaining onions then cheeses, including the Parmesan, on top. Dot with the butter.
Cover the dish tightly with aluminum foil. Bake for 45 minutes (the casserole will be bubbling). Uncover, then bake until onions are soft and silky, and the casserole is golden brown in spots, about 30 minutes more.
Let cool for 10 minutes. Sprinkle with more thyme, then scoop onto plates and serve. If using the lemon, cut the remaining lemon half into wedges for squeezing over the cheesy onions.