Preheat the oven to 400°F. If you're using a baking stone/steel, place the stone/steel in the bottom third of the oven before you start preheating.
Scrub the beets, pat them dry, and place each one on a piece of aluminum foil. Rub the beets a tablespoon or two of olive oil, then wrap the foil around each beet and transfer them to a baking sheet. Roast in the oven for 50 minutes to 1 hour, until the beets are easily pierced with a sharp paring knife. Remove the beets from the oven, unwrap them, and set them aside to cool.
Increase the oven temperature to 500°F (if using a baking sheet) or as high as it will go (if using a baking stone/steel). If you’re using a baking stone or steel, switch the oven to Broil on high as soon as it reaches the higher temperature.
When the beets are cool enough to handle, rub off their skins using a clean paper towel. Trim off the ends, cut the beets into chunks, and transfer them to a food processor or blender. Add 2 tablespoons of olive oil, 1 teaspoon of the chopped dill, and 1 teaspoon of the lemon zest; puree until smooth. Add more olive oil as needed to create a puree with the consistency of thick tomato sauce (I needed another 2 tablespoons). Stir in the vinegar and season with ¼ teaspoon fine sea salt and a few grinds of black pepper.
In a small bowl, stir together the sour cream, horseradish, 1 teaspoon of dill, and 1 teaspoon of lemon zest. Season with ¼ teaspoon fine seal salt and a grind or two of black pepper.
Stretch or roll out your dough to a 12- to 14-inch circle, then transfer it to an oiled or parchment-lined baking sheet or a lightly floured pizza peel (if using a baking stone/steel).
Spoon the beet puree onto the dough and spread it evenly, leaving a ½-inch border all around. Sprinkle some flaked sea salt over top.
Transfer the pizza to the oven and bake until the crust is golden and spotted on the bottom—8 to 10 minutes on the baking sheet, 6 to 8 minutes on the baking stone/steel. Remove the pizza from the oven.
Let the pizza cool for 5 minutes. Measure ½ cup of the horseradish cream mixture into a resealable plastic bag, and snip off the very tip of one of the corners. Pipe the yogurt mixture onto the pizza in a spiral pattern (see photos above), then sprinkle the top with the remaining tablespoon of chopped dill. Cut the pizza into slices and serve with the extra horseradish-yogurt sauce for dipping.