Possibly different booking classes (meaning different earn rates) or a mixed class service?
But I understand what you mean - I was looking at fares on FJ for my one way fare back from the US in January next year (so LAX-NAN-MEL) and while FJ themselves offered it for about $7k, Kiwi.com offered the flight for about $5k (which was still about $1.8K than the SB price from LAX-SYD with a VA business award to shuttle to MEL).
How is Kiwi.com offering the flights for $2k less than FJ themselves? Don't know... (At least the Aircalin flights I booked were also available - separately - through Aircalin themselves for about the same price.)
