Preheat the oven to 400F. Grease a 7-inch round baking dish and set on a baking sheet. Set aside.
In a medium saucepan, cover the unpeeled potato with cold water and bring to a boil. Reduce heat to medium. Cook until just tender, about 25 - 30 minutes. Let cool slightly, then peel and cut into 1/4-inch-thick slices.
Meanwhile, in a large skillet, melt the butter over medium heat. Add the onion and 2 tsp. of kosher salt. Cook, stirring occasionally, until the onion begins to brown, about 8 to 10 minutes. Stir in the sugar, then half of the wine, scraping up the browned bits from the bottom of the pan. Cook, stirring, until the liquid is reduced and the onion is golden, about 8 to 10 minutes. Add the remaining wine. Cook, stirring, until the onion is deep brown and jammy, about 8 to 10 minutes more. Stir in the thyme leaves. Remove from heat.
Arrange half of the potato slices in the prepared baking dish. Season with a bit of salt and pepper. Top with half of the onion. Repeat with the remaining potato slices and onion. Drizzle with the crème fraîche. Top with the cheese slices. Bake in preheated oven until golden-brown and bubbling at the edges, about 15 - 20 minutes. Serve immediately.
You can remove the rind or leave it on, as you like.