Prepare a medium-high gas or charcoal grill fire. Rub the onion slices with 1 Tbs. of the oil, keeping the rings intact, and season with 1 tsp. salt and 1/4 tsp. pepper. Arrange them on the grill in a single layer and cook, flipping once, until lightly charred, 8 to 10 minutes. Transfer the onions to a cutting board and chop into small pieces.
Heat 1 Tbs. of the oil in a medium saucepan over medium-high heat. Add the cumin and pepper flakes and cook, stirring constantly, until toasted and fragrant, about 1 minute. Add the chopped onions, tomato, vinegar, sugar, 1/2 tsp. salt, 1/4 tsp. pepper, and 1/3 cup water. Bring to a boil, cover, reduce the heat to medium, and boil until the onions are soft, 5 to 7 minutes. Uncover the pot and continue to boil, stirring often, until thickened, about 5 minutes more. Season to taste with salt and pepper.
Meanwhile, rub the lamb all over with the remaining 1 Tbs. oil and season with 2 tsp. salt and 1/2 tsp. pepper. Grill, flipping once, until deep golden-brown outside and medium rare inside, about 8 minutes total. Serve topped with the chutney.