Preheat the oven broiler to high and line a baking sheet with foil.
Place the onion wedges and ginger, cut side up, on the baking sheet and broil 10 to 20 minutes until charred; remove ginger earlier if done.
Heat a large pot or Dutch oven over medium heat and toast star anise, cloves, cinnamon sticks, coriander, and fennel seeds for 3 minutes until fragrant.
Add water, charred onions, ginger, mushroom stems, kombu, and tamari to the pot and simmer for 30 minutes.
Strain the broth through a fine mesh strainer into a large heatproof bowl, discarding solids.
In a large skillet over high heat, heat avocado oil and cook shiitake mushrooms with salt for 4 minutes until browned.
Add bok choy wedges cut side down; cook 1 minute, add rice vinegar, cover, reduce heat to medium, and cook 5 to 7 minutes until tender, adding water if dry.
Prepare rice noodles according to package instructions and divide among four bowls.
Add cooked mushrooms, bok choy, and baked tofu to bowls, then ladle hot broth over to cover.
Top with bean sprouts (if using), jalapeños, basil, and cilantro; serve with lime wedges, sriracha, and additional tamari.