Place the halved onion and ginger directly over a gas flame or under a broiler until the surfaces are nicely charred—this adds a deep smoky flavor to the broth. Rinse off any black bits and set aside.
To achieve a clean-tasting broth, add bones to a large pot, cover with water, bring to a boil, and simmer for 10 minutes. Drain and rinse bones under cold water. Clean the pot before returning bones to it.
Add the cleaned bones back into the pot along with charred onion, ginger, spices, fish sauce, salt, sugar, and 10 cups of water. Bring to a boil, then reduce heat and simmer gently for 2.5 to 3 hours. Skim off any foam or fat as needed.
Using a fine mesh strainer or cheesecloth, strain the broth into a clean pot or bowl. Discard solids. Taste and adjust seasoning with more fish sauce or salt as desired.
Cook rice noodles according to package directions, then rinse under cold water to stop the cooking. Arrange sliced beef, bean sprouts, lime wedges, herbs, scallions, and chili on a platter for serving.
Divide noodles among bowls. Place raw beef slices on top (they’ll cook slightly in the hot broth). Pour boiling hot broth over everything. Garnish with herbs and toppings of choice. Serve immediately.