You know that SEG is not imprevious of changes in the middle of the production. Remember Cook Islands? I bet the plan for final 2 not final 3 because when Yul found the hidden idol, it said the idol can be used until final 4. If they plan for final 3, they would say the idol can only be used until final 5.
Of course! I know they come up with stuff on the fly. I think they did the switch in Marquesas on the spot to same Marramu.

and if they're planning that, they would've done it before merge. They wouldn't do double boot after merge. hence James' injury causing final 2. They could've make a reward challenge for the finale, but I guess James' injury makes them think that now they can pull another twist.
The thing that doesn't make sense to me, is, even if you're exactly right about this and it was planned F3 right from the start, James leaving still doesn't make any sense to change it to a F2. Like you said, they'd only need 2 double-boot episodes for a F3, which weren't needed when Jonathan and Kathy left. So, why does James leaving force them to change it to a F2? There is no reasoning behind why his exit would change it to a F2. It doesn't mess the schedule up at all (they could either have James be the only boot that episode, or still have the finale at 4 with a F3 like China). It didn't change the number of jurors. They could easily have had a F3 with James leaving.