Preheat the oven to 425°F and line a large baking sheet with parchment paper.
Peel the beets. Wash and scrub the potatoes but leave the peels on. Chop the beet and potato so they are roughly the same size. Spread the chopped beet and potato on the baking sheet and roast in the oven for 40-45 minutes until you can just pierce the beet with a fork. The larger you chop them the longer they will take in the oven. When the beets and potato are done set aside and begin the soup.
In a large pot, sauté the onion with a few tablespoons of water until the onion begins to soften, about 5 minutes. Add the garlic, thyme, and red pepper flakes and cook for another minute. Now add the roasted beet and potato and vegetable broth and bring to a simmer. Simmer uncovered for a few minutes.
Turn the heat off and transfer the soup to a blender. Add the vinegars and ½ teaspoon salt and blend until smooth. Be careful not to overfill the blender, keep it at about ⅔ full. Blend the soup in batches if you must. Taste and reseason as needed
Pour the soup into bowls right from the blender container or return to the pot and keep warmed on low heat until needed. Add a dollop of thinned sour cream or tahini to each bowl and drag it through to create a swirl effect. Garnish with fresh thyme if desired.