In a very large skillet with a tight-fitting lid, warm the olive oil over low heat and add ¼ cup water. Add the onions, cover the pan, and stir occasionally until onions are softened, about 10 minutes. Add the bay leaves, pepper flakes, and 2 ½ cups of the wine. Cover the pan and simmer gently, stirring occasionally, until the onions are very soft, about 15 minutes.
While the onion/wine mixture is simmering, bring about 4 quarts of water to a boil and add the remaining wine and 1 tablespoon salt. Add the pasta and simmer for 5 to 6 minutes or half the recommended cooking time (see tip below). Drain in a colander, reserving ½ cup of the pasta water.
Dump the drained pasta and reserved pasta water into the pan of simmering wine and onions and bring to a gentle simmer. Cover the pan and allow to simmer, tossing with tongs frequently, until the liquid thickens and the pasta is al dente and most of the wine is absorbed, 6 to 8 minutes. Quickly pull out and discard the bay leaves.
Remove the pan from the heat and add the butter, grated cheese, ½ teaspoon salt, black pepper, and herbs. Toss to coat the pasta thoroughly until the butter pieces are melted. Serve immediately.
For the first cooking of the pasta in Step 2, allow about one-half of the total recommended cooking time. The pasta will finish cooking in the “sauce,” where it will absorb lots of flavor from the wine, and the wine/onion mixture will be enriched and thickened by the starch remaining in the pasta.