Preheat the oven to 375°. On a baking sheet, toss the sunchokes, oil, thyme sprigs and garlic and season with salt. Roast for about 1 hour, stirring occasionally, until golden and tender. Discard the thyme sprigs and garlic. Transfer the sunchokes to a large bowl.
Meanwhile, in a saucepan, cook the vinegar over moderate heat until reduced to 2 tablespoons, 3 minutes. Transfer to a bowl. Stir in the shallots, crushed red pepper and honey.
Wipe out the saucepan. Add the butter and cook over moderate heat until golden brown, 2 to 3 minutes. Whisk the butter into the vinegar mixture and season with salt and pepper.
Add the spinach, chives and vinaigrette to the sunchokes; season with salt and pepper and toss to coat. Serve warm.