Melt 1 tablespoon of the butter in a large sauté pan over medium heat. Add the onion and cook until the slices start to wilt and turn translucent, about 3 minutes. Add the onion soup mix, thyme and 2 tablespoons water. Turn the heat to low, then continue to cook, stirring and adding more water a tablespoon at a time if the mixture gets too dry, until the onions are very soft and golden brown, 5 to 10 more minutes.
Melt 1 tablespoon butter in a saute pan over medium heat. Spread 1 teaspoon mustard onto one side of each slice of bread. Divide the Cheddar, Gruyere, caramelized onions and crispy onions between 2 of the slices of bread on top of the mustard. Top each with another slice of bread, mustard-side in, and lay the sandwiches in the pan. Cook, pressing down on top of the sandwiches, until the bottoms are golden brown, about 2 minutes. Add the remaining 1 tablespoon butter to the pan and flip the sandwiches, cooking until the cheese is melted and the bottoms are golden brown, about 3 more minutes. Cut in half and serve.