Fill a pot with about 6 quarts of water and bring to a boil.
Pour about 1 inch of water in a second pot, one that's large enough to contain the spinach, and bring to a boil. Add 1 teaspoon salt and the spinach and cook until quite tender, 5 to 6 minutes.
Drain the spinach in a colander, pressing on it with the back of a spoon to squeeze out as much water as possible. Transfer the spinach to a cutting board and finely chop it.
Meanwhile, peel and finely chop the onion. Place the butter and onion in a large skillet over medium-high heat and sauté until the onion turns a rich golden color, about 5 minutes.
When the water for the pasta is boiling, add 2 tablespoons salt and the penne and stir well. Cook until al dente.
When the onion is ready, add the spinach to the skillet and sauté, stirring often, for about 5 minutes. Add the ricotta, cream, and nutmeg, and cook, stirring, until the ricotta is heated through and the cream has reduced considerably, 2 to 3 minutes. Taste and season accordingly with salt and pepper, then remove from the heat.
When the penne is done, drain it well, toss it with the spinach and ricotta sauce and the Parmigiano-Reggiano, and serve at once.