Preheat oven to 400 degrees. Toss sweet potato with 1/2 teaspoon oil and 1/4 teaspoon salt; spread in an even layer on half of a rimmed baking sheet. Toss beets with 1/2 teaspoon oil and 1/8 teaspoon salt; spread on other half of sheet (so that beets don't discolor potatoes). Roast, stirring halfway through, until tender, 35 to 40 minutes.
Meanwhile, bring a large saucepan of water to a boil; add vinegar. Break each egg into a teacup. Reduce heat so that water is just simmering. Slightly immerse 1 teacup, and gently slide egg into water. Use a spoon to fold edges of white over egg. Repeat with remaining eggs. Simmer until whites are just set but yolks are runny, 2 to 3 minutes. Transfer eggs to a towel using a slotted spoon, and drain.
Thinly slice beet greens. Heat 1 1/2 teaspoons oil in a large nonstick skillet over medium heat. Add greens, leek, 1/4 teaspoon salt, and 1/4 teaspoon pepper; cook until tender and lightly browned, 8 to 10 minutes. Stir in quinoa, thyme, and vegetables; press down using a rubber spatula. Cook until quinoa is warm, 1 to 2 minutes. Divide among 4 plates; top each with 1 egg, and season with a pinch of pepper.