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Heat the olive oil in a large Dutch oven or heavy-bottomed pot over medium heat.
Add the diced yellow onion, carrots, and celery; cook until softened, about 8–10 minutes.
Push the vegetables to one side of the pot and add the ground beef on the other side; break it up and cook until browned all over, about 8–10 minutes. Drain excess fat and stir the beef with the vegetables.
Stir in the minced garlic and cook until fragrant, about 1 minute.
Pour in the red wine, scrape up any browned bits from the bottom of the pot, and simmer until reduced by half, about 5–7 minutes.
Add the whole milk and bring to a gentle simmer; cook until almost all the milk has evaporated, about 10–15 minutes.
Stir in the crushed tomatoes, beef broth, bay leaf, and freshly grated nutmeg. Season with salt and freshly ground black pepper to taste.
Bring the sauce to a gentle simmer, reduce heat to low, partially cover, and cook for 1½–2 hours, stirring occasionally.
About 15 minutes before serving, bring a large pot of salted water to a boil. Add the rigatoni and cook until al dente according to package directions; reserve 1 cup of pasta cooking water before draining.
Drain the rigatoni and add it directly to the Bolognese sauce; stir to coat, adding reserved pasta water as needed to reach desired consistency.
Serve immediately topped with freshly grated Parmesan cheese and a sprinkle of fresh parsley, if desired.