Whisk the pineapple juice, soy sauce, rice vinegar, brown sugar, garlic, ginger, sesame oil, lime zest, and red pepper flakes (if using) in a large measuring bowl until the sugar dissolves. Set aside 1/3 cup of this mixture for the glaze.
Place the chicken pieces in a large zip-top bag or bowl. Pour the remaining marinade over the chicken, seal, and toss to coat. Refrigerate for at least 2 hours (up to overnight for deeper flavor).
If using wooden skewers, soak them in water for 20 minutes so they don’t scorch. Prep the pineapple and red onion into 1-inch chunks while the chicken marinates.
When ready to cook, preheat the grill to medium-high heat (425–450°F). Clean and oil the grates with the neutral oil.
Thread the marinated chicken, pineapple, and red onion onto skewers, alternating for even cooking. Lightly shake off excess marinade from the chicken to minimize flare-ups.
Make the glaze: Bring the reserved 1/3 cup marinade to a simmer in a small saucepan over medium heat for 2–3 minutes. Stir in the cornstarch slurry and cook, whisking, until glossy and slightly thickened, 1–2 minutes. Remove from heat.
Grill the skewers over direct heat with the lid closed, 5–6 minutes. Flip and cook another 4–6 minutes, brushing with the glaze during the last 3 minutes. Cook until the chicken is lightly charred in spots and reaches 165°F at the thickest piece.
Transfer to a platter and rest 3 minutes. Garnish with green onions and sesame seeds, and serve with any remaining glaze for dipping.