1. Place each variety of beet in a separate saucepan; divide fennel slices, garlic, apple pieces, 4 sprigs of thyme, bay leaves, and 2 tablespoons salt evenly between saucepans. Add enough water to each saucepan to cover contents by 4 inches. Place each saucepan over high heat and bring to a boil; immediately reduce heat to a simmer and cook until beets are easily pierced with the tip of a knife, 25 to 35 minutes. Drain and discard all contents except for beets.

2. Peel and quarter beets. Transfer each variety to its own bowl. Toss each with 2 tablespoons olive oil and season with salt and pepper; set aside.

3. Place flour in a shallow dish and season with salt. Add shad roe and gently toss to coat, shaking off excess. Transfer to a plate and set aside.

4. Place bacon slices in a large nonstick skillet and cook over medium heat until bacon is crisp and fat has been rendered. Remove bacon from skillet and set aside. Remove all but 3 tablespoons bacon fat and discard. Add 3 tablespoons olive oil, shad roe, and remaining 2 sprigs thyme to skillet. Cook for 1 minute and turn; add butter and continue cooking until shad roe reaches an internal temperature of 135 degrees on an instant read thermometer, 1 to 2 minutes more. Remove from heat and set aside.

5. To serve, divide beets, bacon, and frisee evenly between 4 plates. Place shad roe on each plate and sprinkle with sea salt and chopped herbs. Drizzle with remaining 1/4 cup olive oil and balsamic vinegar before serving.