Preheat oven to 350 degrees. Cut onions into flowers: Make 4 vertical cuts going only part way through each unpeeled onion to create 8 wedges that are still attached to the root end. Remove papery skins. Cut a very small slice off the root end off the onions so that the onions can stand up in an 9 x 13-inch oven safe baking dish. Pour water, miso, and butter into a small saucepan and heat on medium high until miso and butter melt. Pour miso mixture over onions, cover with foil and bake for 30 minutes. Uncover and bake an additional 10 minutes or so until the onions bloom. Some may not open on their own and will need a little coaxing once plated.
As the red onions bake, pan fry the green onions with a small amount of oil until the bulbs are slightly browned and the greens are wilted. Remove from pan and dip the bulb ends into black sesame seeds to mimic dirt clinging to freshly picked bulbs. Arrange on serving platter and set aside.
Transfer onion blooms to the serving platter, top with chopped cilantro for garnish. Pour miso butter over onions and serve.