Fill a large pot three-quarters full with cold water and add the beets. Sprinkle the water generously with kosher salt. Bring to a boil over medium heat, and then reduce the heat and simmer gently until the beets are tender when pierced with the tip of a knife, 30 to 35 minutes. Drain and let cool for about 10 minutes.
Peel the beets by "wiping" the skin off with a kitchen towel. Trim the tough parts of the tops and bottoms with a small knife and cut each beet into 6 to 8 wedges, like wedges of an orange.
Place the beets in a bowl. Whisk together the cider vinegar, balsamic vinegar, pomegranate molasses, brown sugar and sea salt and pepper to taste in another bowl until the sugar dissolves. Add the beets and toss thoroughly to coat. Marinate in the refrigerator for 10 to 15 minutes.
When ready to serve, add the olive oil and stir to coat the beets. Taste for seasoning, adding more sea salt and pepper if needed. Top with the pepitas.