Set a sous vide immersion circulator to 130°F (54°C) in a pot of water.
Season the scallops lightly with salt. Place them in a vacuum-seal or zip-top bag with the butter, thyme, and garlic.
Submerge the bag in the water bath and cook for 30 minutes.
While the scallops cook, toss the already-cooked beets with the olive oil, vinegar, honey, salt, and pepper. Let sit at room temperature.
Remove the scallops from the bag, reserving the butter, and pat them completely dry with paper towels.
Heat the oil in a heavy skillet over high heat until almost smoking. Sear the scallops for 45 to 60 seconds per side, until deeply golden.
Divide the beets among plates, top with the seared scallops, and drizzle with the reserved butter. Finish with dill, flaky salt, and lemon wedges.