Butter an ovenproof 4-quart casserole dish. Set aside.
Preheat oven to 350 degrees.
In a large bowl, whisk together the flour, salt, pepper, and nutmeg.
Add the beaten eggs, beef broth, and some (possibly all) of the water.
Whisk until it's the consistency of pancake batter with no lumps.
In a large stockpot, bring 6-8 cups of lightly salted water to boil.
Working in batches, add the spaetzle batter into a spaetzle maker (or colander) over the pot of boiling water.
Allow the batter to fall into the boiling water in droplets, stirring so they don't clump together.
Once the spaetzle plump and float to the surface, remove them from the water using a large slotted spoon.
Place one layer of cooked spaetzle in the bottom of the prepared casserole dish, and drizzle one-third of the melted butter over top.
Layer one-third of the grated cheese evenly over the spaetzle, and one-quarter of the crispy onions.
Continue the same process with the remaining spaetzle batter, butter, cheese, and onions, ending with a layer of cheese to finish.
Place the casserole in a preheated oven (covered) for 20 minutes.
Top the casserole with additional crispy onions and serve hot.