In a small bowl, combine 1 Tbsp. of the olive oil, vinegar, maple syrup, mustard powder, garlic, ¼ tsp. salt, and chili flakes; stir with a whisk. Set aside.
Heat remaining 2 Tbsp. oil in a large skillet over medium heat. Once hot, add Brussels, toss in oil, and cover pan with lid. Cook Brussels, lifting the lid to stir every 2 to 3 minutes, until tender and golden brown, about 8 minutes. Season with remaining ¼ tsp. salt and black pepper.Add Maple-Mustard glaze to pan, along with pumpkin seeds and fresh thyme; toss to coat. Cook 1 to 2 more minutes, stirring often, until the glaze caramelizes the sprouts.
Transfer Brussels to a serving dish and scatter cheese overtop, allowing residual heat to slightly melt cheese. Serve warm.
