This is what happened two days ago when I flew from Hong Kong to Yogyakarta.
Check in was a zoo in Hong Kong. There were two tour groups returning to Indonesia (to Yogyakarta actually) and they took a long time to process. Then Jardine Aviation Services (ground agent) used a number of new, inexperienced staff members so exceptional cases took longer to process. We were told at check in that we would not see bags in CGK. They issued boarding pass for CGK to YOG in HKG also and we were told to simply go through immigration at CGK.
In flight - the B737-800 all had AVOD which was working already when we boarded the plane. Choice of entertainment was OK. For a 0900 departure with 1300 arrival in CGK, we were served a lunch, with shrimp salad appetizer, fish on rice with veggies, and coconut cake for dessert. Definitely can't expect similar AVOD and food on Cathay.
Seats were a bit cramped with 31 inches of legroom.
At CGK, we were hard pressed to use up all the three hours we had. In Terminal 2E where all GA international flights land, Indo citizens use the immigration counters AT THE END of the corridor, foreigners use the counters ON THE SIDE. Those who need to buy visa on arrival do not have to queue up separately. Because few foreigners travel on GA, the immigration line was extremely short. We took time to walk up to the counters, and were THE LAST to go through immigration. By the time we walked into baggage terminal (and we did not have to retrieve bags), walked to the end of the baggage terminal (without exiting into the common area), and took the escalator upstairs to the departure area for terminal 2F (domestic terminal), it only took 35 minutes max. If GA allowed a 60-minute connection for INTL-DOM flight if passengers are travelling GA all the way, we could have taken the 1415 flight to YOG instead of waiting for the 1615 flight.
Our 1615 flight to YOG was delayed by about 40 minutes. However, they decided to distribute snack boxes at the gate because the flight was late. AND THEN, we were given another snack box on our flight ! Not bad for being apologetic.
Bags arrived in YOG and they "did not have to go through customs". I am sure the bags were x-rayed in CGK before being loaded onto the domestic flight and if something was wrong, passengers would have been called to open them.
Pleasantly surprised and would take GA again next time going to Indonesia.