Combine pineapple juice, orange juice, vinegar, sugar, ketchup, red pepper flakes, and 1/8 teaspoon salt in a medium saucepan. Bring to a boil over medium-high heat. Reduce heat to medium and simmer for 8 to 10 minutes or until reduced to 1 1/2 cups.
Dissolve 1 tablespoon cornstarch in 1 tablespoon of water and add to sauce. Cook until thickened, about 1 minute. Set sauce aside.
Set a wire rack in a rimmed baking sheet and cover half of rack with paper towels.
Cut chicken crosswise into 1/2-inch wide strips on a slight bias. Cut long strips in half. Pat dry with paper towels. Season chicken with salt and pepper.
In a large bowl, whisk together flour, cornstarch, baking powder, baking soda, 2 teaspoons salt, and 1 teaspoon pepper.
Whisk in water and 3 tablespoons oil until smooth. Place chicken in batter and stir to coat all pieces.
Pour 1 1/2 inches oil into a Dutch oven. Heat oil to 375 degrees.
Use a fork to spear chicken pieces and another fork or spoon to slide chicken off fork and into oil. Fry in batches and do not crowd pan. Keep oil temperature between 350 and 375 degrees.
Fry for 2 to 3 minutes, until golden and cooked through.
Place chicken on paper towel-lined rack. Once paper towels have absorbed excess oil, move to side of rack without paper towels.
Once all chicken is cooked, turn heat off and add peppers and red onion to oil. Fry for 1 minute and remove to a paper towel-lined plate.
Add green onions to oil for 5 to 10 seconds and transfer to plate with peppers and red onion.
Reheat sauce and toss 1 cup of sauce with chicken, red pepper, and both onions.