Place water and kombu in a pot over low heat. When water is hot but not boiling, remove from heat and add bonito flakes. Stir briefly and let sit about 1 minute. Strain through a fine sieve into a clean pot, discarding kombu and bonito flakes. Add tamari, mirin, sake, wakame, and tofu.

Reheat soup to a bare simmer, stirring gently from time to time. Scoop out 1 cup broth and place in a small bowl; add miso and mix until smooth. Remove soup from heat and stir in miso mixture. Adjust seasoning by adding more tamari and mirin, as desired. Serve at once, garnished with sliced scallions.