I agree with the recommendation of the ship. Fly Manado to Sorong on the 15h. Stay one night in a hotel then go to the ship. Best thing to do in Sorong? Read a book, watch a movie, assemble & test an underwater camera rig, sleep.
If the ship's people ask you to arrive a day early, you should do what they ask. I'm happy to hear that they recognize the potential problem and try to help their guests avoid delays in the ship's departure (and so you do not miss part of the trip).
Captain Hook wrote: "But NO operator to my knowledge has EVER left a guest behind because of their flights ... and I think it would be an absolute outrage if they did. "
Depends on the point of view.. that of the late diver or the divers who arrived on time who are waiting and missing dives in Raja Ampat (as mentioned by rusti999).
My opinion is different. I think it not fair (outrageous?) to deprive on-time guests of diving in Raja Ampat they've all paid for ($$$$) because of a late arriver.
------
My thoughts on this are based on my experiences organizing trips to Raja Ampat for groups and individuals for 13 years.
1. Flights between Manado and Sorong are not as reliable as Jakarta-Sorong or Makassar (UPG) - Sorong. Jakarta or Makassar routes offer more flights per day, earlier arrival times so that flights are less likely to be delayed 'til the next day, fewer cancellations or delayed bags (depending on airline and route of course.. but there are choices of less risk via Jakarta & Makassar).
2. Knowing that airlines (not only in Indonesia but in Europe, USA, etc.) often cancel flights or flights are late, travelers should schedule plenty of connection time and plan to arrive early for ship departures. This includes International flights as well as flights within Indonesia.
3. Arriving late impacts not only the person who is late, but also all the other guests booked onto the trip. The only benefit would seem to be to the liveaboard owners since it could eliminate one day of motoring (and fuels costs) around Raja Ampat to stay near Sorong waiting for late guests. Should a liveaboard that has a load of guests who did choose a less risky route or airline or to arrive early and stay overnight in Sorong deprive on-time guests of a day of diving in Raja Ampat to wait on late guests?
------------
My experience with groups and the Manado - Sorong route is that 50% of the time either the flight is canceled or some bags do not arrive. Using route Jakarta - Sorong or UPG - Sorong there have been no cancellations or delayed bags in 13 years.
This month, Dec 2011, the group FOLLOWING my last group booked Manado - Sorong. Big aircraft. Their flight was canceled and they were rerouted via UPG. They lost one day diving Raja Ampat. Then their return flight was canceled too. The airline offered a return 2 days early or one week later than the ticket they purchased. After some argument with that airline by their travel agent (Indonesian agent) they were offered a flight on a different airline at no extra cost on the original date of their ticket.
If the flight Manado - Sorong is cancelled it may come the next morning or the passenger may have to change airlines or route another way so that they arrive the next afternoon or 2 days later.
If bags Manado - Sorong or Sorong - Manado are delayed the next chance to get bags is on the next flight by that same airline which may be 2 days later.
On the trips I organize we board the ship at 9AM on departure day and leave port shortly thereafter.. we are diving on the first day 2-3 dives.
My recommendation for my own groups is to arrive in Sorong the day before ship departure if coming via Jakarta or Makassar (UPG) or two days before ship departure if coming from Manado. Also if diving in the Manado area, schedule that diving AFTER the liveaboard trip in Raja Ampat if at all possible. If the Sorong-Manado flight is delayed, then a call to the resort for a later pickup is all that is needed.. and if bags are delayed the resorts can provide rental gear until the bags arrive.
If someone arrives in Sorong late and the ship is far away when they arrive, a speedboat can be arranged to bring the late diver to the ship. Meanwhile the rest of the group will be enjoying their dives in Raja Ampat.. what they paid for! Travel insurance will cover the cost of the speedboat. We will help with speedboat arrangements and leave a crew member in Sorong to meet them at the airport and escort them to the ship.
Obviously things change if ALL guests are late!
I call myself paranoid for analyzing risk of flight delays, etc. One of my guests calls it a touch of OCD.