Heat oil in a large nonstick pot over high heat. Add onions and ginger, cut side down. Cook without moving until deeply charred with blackened spots, about 4 to 5 minutes. Flip and char the other side for another 2 to 4 minutes. (This builds deep flavor in the broth quickly.)
In a separate dry skillet, toast star anise, cinnamon, cloves, fennel seeds, and coriander seeds over medium heat for 1 to 2 minutes, until very fragrant. Transfer right away to a plate or bowl to stop the cooking.
Add chicken broth, chicken thighs, toasted spices, 1/2 the bunch of cilantro (stem and leaves), and sugar to the pot with the charred aromatics. Bring to a gentle simmer, then reduce heat to low. Partially cover pot with a lid and simmer gently for 35 to 45 minutes. Skim off any foam that rises to the top and discard.
Transfer chicken to a plate. Once cool enough to handle, shred the meat and discard skin and bones.
Strain the broth through a fine mesh strainer into a clean pot. If desired, add fish sauce to taste, about 1 up to 2-1/2 tablespoons, then add salt if needed. The broth should taste slightly salty since it will dilute once the noodles are added. Keep warm until ready to serve.
Cook rice noodles according to package directions. Drain well, rinse briefly in cold water, and shake off excess water.
Divide noodles between bowls. Top with shredded chicken and green onions. Ladle hot broth over everything. Finish with desired toppings, including the reserved cilantro. Squeeze fresh lime juice over bowls just before eating.
Notes
Storage: Store broth and chicken together in the fridge for up to 4 days. Keep noodles and toppings separate and add fresh when serving.