In a large stockpot, bring enough water to a boil. Add beef bones and brisket and boil for 10 minutes to release impurities. Drain, rinse the bones and meat under cold water, and clean the pot.
In a dry skillet over medium heat, lightly toast ginger, lemongrass, garlic, cinnamon, and cloves for 2–3 minutes until fragrant. Wrap toasted spices in cheesecloth or place in a spice bag.
Fill the clean pot with 7 quarts of water. Add bones, brisket, and spice bag. Bring to a gentle boil, then lower to a simmer. Add the whole onion and simmer uncovered for about 90 minutes, skimming foam and excess fat occasionally. Remove the brisket when tender and set aside to cool. Discard the onion and spice bag. Keep broth warm on low.
In a small saucepan over medium-low heat, warm sesame oil. Add annatto seeds and steep for about 5 minutes until oil turns deep red-orange. Strain seeds and return oil to the pan. Add minced garlic and shallots; sauté for 3–4 minutes until golden. Set aside.
In the same pan, heat 2 tablespoons of sesame oil. Add crushed red pepper flakes, minced lemongrass, and shrimp paste. Cook for 3–4 minutes over medium heat until fragrant, stirring. Remove from heat and stir in chicken bouillon powder, kosher salt, and fish sauce.
Cook thick rice noodles according to package directions, rinse in cold water, and set aside. Slice mushrooms and onions; shred water spinach and cabbage. Thinly slice cooled brisket for topping.
Reheat broth to a gentle simmer and stir in the seasoning base to taste. Adjust salt and fish sauce as needed. To assemble: place warm noodles in bowls, add mushrooms, brisket slices, and raw tenderloin. Ladle very hot seasoned broth over the raw tenderloin so it cooks gently. Drizzle with aromatic oil and top with green onions, bean sprouts, oregano, and lime wedges.
Notes
Adjust the heat level by varying the amount of crushed red pepper flakes.
Feel free to customize the toppings based on your preference.