Preheat the oven to 400 degrees F. Butter a small baking dish, similar to 6x8.
Start by making the caramelized onions. Melt the butter in a skillet over medium heat, then add the onions. Season the onions with Kosher salt and cook until brown and caramelized—about 30 minutes.
Layer the spätzle in the baking dish. Add half the cooked spätzle, followed by half of the caramelized onions. Season with salt and pepper, and add half of the shredded cheese. Repeat.
Bake for 15-20 minutes until the cheese is melted and the edges are just beginning to get a little brown and crispy.
Serve immediately.