Preheat oven to 400°F.  Grease a 9 x 13-inch baking dish with cooking spray; set aside.

Melt the butter in a large sauté pan over medium-high heat.  Add the onion, and sauté for 4-5 minutes until soft and translucent.  Add the garlic and sauté for an additional 1-2 minutes until fragrant.  Stir in the gluten free flour until it is evenly combined, and cook for 1 more minute.  Gradually pour in the vegetable stock, and whisk until combined.  Add in the milk, salt, pepper, and 1 teaspoon thyme, then whisk until combined.  Continue cooking for an additional 1-2 minutes until the sauce just barely begins to simmer around the edges of the pan and thickens.  Then remove from heat and set aside.

Spread half of the sliced potatoes in an even layer on the bottom of the pan.  Top evenly with half of the cream sauce. Then sprinkle evenly with 1 1/2 cups of the shredded Emmi Le Gruyère AOP, all of the Parmesan cheese.  Top evenly with the remaining sliced potatoes, the other half of the cream sauce, and the remaining 1 1/2 cups of Emmi Le Gruyère AOP cheese.

Cover the pan with aluminum foil and bake for 30 minutes.  The sauce should be nice and bubbly around the edges.  Then remove the foil and bake uncovered for 25-30 minutes, or until the potatoes are cooked through.

Transfer the pan to a cooling rack, and sprinkle with the remaining teaspoon of thyme, flaky sea salt, and freshly ground black pepper  Serve warm.