I think Neobie's point is that why would you fly from Bangkok to Phuket and then continue to Koh Samui when you could have just got straight from BKK to Koh Samui?
For the same reasons I have to fly through Chicago or Denver to get to New York, even though I could go straight from LAX to NYC on a nonstop flight.
-availability
-price
-convenience/departure times
Of course we'd all love to fly nonstop whenever it's an option, but often times we don't for any or all of the above reasons. Production doesn't have an unlimited budget and the nonstop flights from Phuket to Ko Samui are very cheap ($89).
ETA:
Here's an example to illustrate my point. Flight search for a one way ticket from Jakarta to Ko Samui departing later this week:
$664 is cheapest option, and all flights with this price are via Phuket
$995 is the price to fly through Bangkok (!!) and this itinerary would be ~6.5 hours, only around two hours shorter than the cheaper option through Phuket (~8.5 hours)
I think if WRP could save $1000 by having a team and one production person take the first option, it makes perfect sense.
That's odd ?
I get a routing from Jakarta to BKK to Koh Sumui for $974 that looks like this
Thai Airways  Flight 434    3h 30m
     Take-off    Fri 12:35p    CGK    Jakarta, Indonesia
     Landing    Fri 4:05p    BKK    Bangkok, Thailand
     Coach  |  Airbus A330-300 (Wide-body Jet)  | 3h 30m  | 1444 miles
     Connection    BKK    Bangkok, Thailand    4h 55m
   Bangkok Airways  Flight 199    1h 00m
     Take-off    Fri 9:00p    BKK    Bangkok, Thailand
     Landing    Fri 10:00p    USM    Ko Samui, Thailand
     Coach  |  Airbus A319 (Narrow-body Jet)  | 1h 00m 
And the only routes that do include Phuket also happen to go through KUL and those are coming in at $664.  They look like this:
Malaysia Airlines  Flight 710    2h 00m
     Take-off    Fri 11:10a    CGK    Jakarta, Indonesia
     Landing    Fri 2:10p    KUL    Sepang, Malaysia
     Coach  |  Boeing 737-800 (Narrow-body Jet)  | 2h 00m
     Connection    KUL    Sepang, Malaysia    
3h 00m
   Malaysia Airlines  Flight 790    1h 15m
     Take-off    Fri 5:10p    KUL    Sepang, Malaysia
     Landing    Fri 5:25p    HKT    Phuket, Thailand
     Coach  |  Boeing 737-400 (Narrow-body Jet)  | 1h 15m
     Connection    HKT    Phuket, Thailand    
1h 40m
   Bangkok Airways  Flight 258    0h 55m
     Take-off    Fri 7:05p    HKT    Phuket, Thailand
     Landing    Fri 8:00p    USM    Ko Samui, Thailand
     Coach  |  Aerospatiale/Alenia ATR 72 (Turbo-prop Plane)  | 0h 55m 
But since we know the racers were spotted on a flight from BKK and not from KUL we can conlude that they were not continuing to Koh Sumui.