Soak the beans: Place dried beans in a large bowl and cover with cold water (~ 8 cups/2 L). Add the salt and baking soda. Cover and soak for 8 to 12 hours, or overnight. Drain and rinse well. See Note 5 for a quick soaking.
When ready to cook, arrange a rack in the middle of the oven and preheat to 350ºF (175ºC).
In a Dutch oven or large ovenproof soup pot, heat 1 ½ tablespoons olive oil over medium. Once hot, add the onions, carrots, and celery with a big pinch of salt. Cook, stirring occasionally, until softened, about 10 minutes. Add the red pepper flakes, if using, and stir frequently for 30 seconds.
Pour in 6 cups (1.5 L) water, the drained beans, ½ tsp kosher salt, and lots of pepper (if not using Better than Bouillon, use 1 tsp kosher salt). Partially cover and bring to a boil.
Meanwhile, make the Bouquet Garni: using kitchen twine, tie together the rosemary and sage sprigs plus bay leaves.
Once it comes to boil, add the Better than Bouillon and stir thoroughly to dissolve. Add the bouquet garni and submerge in the liquid. Boil uncovered for 10 minutes. Meanwhile, peel the papery outer skins from the garlic but leave the heads intact. Slice off ~ ¼ inch (0.5 cm) from the top of each head to expose the cloves, as if roasting whole garlic.
Once the beans have boiled for 10 minutes, turn off the heat. Add in the garlic heads. Pour a glug of olive oil (~ 2 tablespoons) on top of the garlic and beans. Cover the pan.
Bake in the oven until the beans are tender, 60 to 75 minutes (for small beans, like navy beans, check around 45 minutes; see Note 6).
Pick out the bouquet garni (discard) and garlic heads (keep these). Scoop a ladle of hot broth into a glass. Add the miso to the hot broth; whisk well until miso is dissolved. Pour miso broth into the soup and stir well.
If the soup is too thick for your liking, add ½ to 1 cup (120 to 240 mL) of freshly boiled water.
Once cool enough to touch, squeeze garlic cloves out of their skins and into the soup, stirring well. Drizzle in 1 tablespoon of good-quality olive oil and season with salt and pepper to taste. Taste, adding more olive oil for richness.
Once cooled, store the soup in a storage container for up to 5 days in the fridge, or freeze for up to 6 months.