Peel and finely chop the lemongrass after removing the dark, fibrous parts, keeping the white and light green portions.
In a large bowl, whisk together vinegar, calamansi juice, garlic, ginger, lemongrass, sugar, salt, and pepper until well-blended.
Add chicken to the marinade, cover the bowl, and let it marinate in the refrigerator for at least 2 to 4 hours.
In a wide pan over medium heat, cook chicken fat until crisp and oil is rendered. Remove skin and bottoms using a slotted spoon.
Lower heat and add annatto seeds, crushed garlic, and bay leaf. Cook for 1 to 2 minutes, turning to prevent seeds from burning.
Remove the pan from heat and let the oil steep for about 1 hour until it has a deep orange color. Strain the oil using a fine-mesh sieve, discarding aromatics, and set it aside.
Lightly grease grill grates and heat over hot coals.
Drain chicken from the marinade and scrape off any stray aromatics. Arrange chicken on hot grates with the skin side up.
Grill chicken, turning and basting regularly with half of the chicken oil, for 30 to 40 minutes or until a thermometer registers 160°F in the thickest part of the chicken.
Remove from heat, cover, and let it rest for 3 to 5 minutes. Serve hot with the remaining chicken oil and steamed rice.