In a large stockpot, bring enough water to a boil. Add the beef bones and brisket, and boil for 10 minutes to remove impurities. Drain and rinse the meat and bones under cold water. Clean the pot.

In a dry skillet over medium heat, lightly toast the ginger, lemongrass, garlic, cinnamon stick, and cloves for 2–3 minutes until aromatic. Wrap the toasted spices in cheesecloth or place in a spice bag for easy removal.

Fill the clean pot with 7 quarts of water. Add the bones, brisket, and spice bag. Bring to a gentle boil, then reduce to a simmer. Add the whole onion to the pot and simmer uncovered for about 1½ hours, skimming any foam or excess fat that rises to the top. Once the brisket is tender, remove it and set aside to cool. Discard the onion and spices. Keep the broth warm over low heat.

In a small saucepan, heat the sesame oil over medium-low heat. Add the annatto seeds and let them steep for about 5 minutes until the oil turns a deep red-orange. Strain and discard the seeds, then return the infused oil to the pan.

Add minced garlic and shallots to the infused oil. Sauté for 3–4 minutes until golden and fragrant. Set aside.

Using the same pan, heat 2 tablespoons sesame oil. Add crushed red pepper flakes, minced lemongrass, and shrimp paste. Cook for 3–4 minutes over medium heat until fragrant, stirring often. Remove from heat.

To the warm broth, add the seasoning mixture and stir well to combine. Add the sliced tenderloin, mushrooms, and thinly sliced onion into the broth. Allow the soup to simmer until the beef is cooked and the mushrooms are tender.

Prepare the rice noodles according to package instructions. Drain and divide among serving bowls.

Ladle the hot soup over the noodles, making sure to include plenty of beef and mushrooms in each bowl.

Garnish with water spinach, banana blossom, bean sprouts, fresh oregano leaves, and red cabbage if using. Serve with lime wedges and the dipping sauce on the side.