Combine 2 cups soy sauce, cane vinegar, black pepper, sliced onion, and 1 cup water in a large bowl to make the marinade.

Add chicken to the marinade and cover the bowl with plastic wrap.

Refrigerate for at least 8 hours or overnight to marinate the chicken.

Prepare the dipping sauce by stirring together the remaining soy sauce and chopped onion with lemon juice, scallions, chili flakes, and 1/2 cup water.

Set the dipping sauce aside.

To make the red rice, combine jasmine rice, ground annatto seeds, and 5 cups water in a 4-qt. saucepan.

Bring to a boil over medium-high heat, then reduce heat to medium-low.

Cook, covered, until rice is tender, about 10 to 12 minutes.

Remove the rice from the heat and keep warm.

Build a medium-hot fire in a charcoal grill or heat a gas grill to medium-high.

Alternatively, heat a cast-iron grill pan over medium-high heat.

Cook the chicken on the grill, turning, until well-browned and cooked through.

Serve the grilled chicken with red rice and dipping sauce on the side.