Char the yellow onion and fresh ginger over an open flame or under a broiler until the skins are blackened and fragrant.
In a large heavy-bottomed pot, toast the star anise and cinnamon stick over medium heat for 1 minute until their scent blooms.
Add the beef bone broth, charred onion, charred ginger, and coconut aminos to the pot and bring to a gentle simmer for 20 minutes.
While the broth develops flavor, soak the dry rice stick noodles in hot water according to package directions until tender, then drain and set aside.
Thinly slice the beef eye of round against the grain into paper-thin pieces to ensure they cook quickly in the hot broth.
Strain the broth through a fine-mesh sieve to remove the solids and return the clear liquid to the pot, seasoning with sea salt.
Divide the cooked noodles between large serving bowls and arrange the raw beef slices in a single layer on top of the noodles.
Pour the boiling hot broth directly over the beef slices to cook them instantly, then garnish with bean sprouts, Thai basil, jalapeño, and a squeeze of lime.