This is my understanding - example HKT-BKK-SIN
At HKT, you have a choice of:
(A) Fly to BKK domestically
(B) Fly to BKK internationally by clearing exit passport control in HKT
The HKT-BKK plane arrives at BKK domestic gate, but you're transit experience differs in:
(A) Exit gate area, pick up luggage (?), check-in at counter (?), queue for exit passport control, queue for security, arrive at BKK-SIN gate area
(B) queue for CIQ security, arrive at BKK-SIN gate area (You can only do this because your passport has a CIQ sticker)