01 - Preheat oven to 375°F. Grease a 9x13-inch baking dish with butter or cooking spray.
02 - Melt 2 tbsp butter in a large skillet over medium heat. Add sliced onions and a pinch of salt. Cook, stirring frequently, until onions are deeply golden and caramelized, about 20-25 minutes. Add minced garlic during the last minute and remove from heat.
03 - In a small saucepan over medium-low heat, combine heavy cream, whole milk, dried thyme, ground nutmeg, black pepper, and remaining 1 tbsp butter. Heat until steaming but not boiling. If using flour, whisk it in until smooth and slightly thickened.
04 - Arrange half of the sweet potato slices in the prepared baking dish, overlapping slightly. Season lightly with salt.
05 - Spread half of the caramelized onions evenly over the potatoes. Sprinkle with half of the Gruyère and half of the cheddar cheese.
06 - Repeat with remaining sweet potato slices, caramelized onions, and cheeses.
07 - Carefully pour the warm cream mixture evenly over the layered ingredients, ensuring coverage across the entire dish.
08 - Cover baking dish tightly with aluminum foil. Bake for 40 minutes until potatoes begin to soften.
09 - Remove foil and continue baking uncovered for 20 minutes, or until the top is golden brown and bubbly, and potatoes are fork-tender.
10 - Let gratin rest for 10 minutes before serving to allow layers to set. Garnish with chopped fresh chives if desired.