Step 1 Combine the onion powder, garlic powder, cayenne, red pepper flakes, about 1 tablespoon salt and 1/2 teaspoon freshly ground pepper in a bowl. Rub the mixture over the tri-tip to cover the surface evenly. Top with the sliced onion, chopped garlic and thyme, cover the bowl and refrigerate at least 2 hours, up to overnight.
Step 2 Transfer the tri-tip and the rest of the ingredients from the bowl to a sealable plastic bag. Add the olive oil and vinegar, press out any air, seal tightly and then rub to distribute evenly over the surface of the meat. Refrigerate at least 6 hours or overnight.
Step 3Grill over high heat, searing both sides, then move to a cooler spot on the grill and cook, turning frequently, until well-browned and medium-rare to medium (about 130 degrees), 30 to 40 minutes. The meat should feel firm but still give with pressure.
Step 4Set aside to rest at least 10 minutes before carving. Slice it thin, across the grain, holding the knife at a slight angle to make wider slices.