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Yes that's what I assumed. Using chromakeying that would be pretty easy as the window itself makes for a perfect "frame" that the screen would sit behind, and then get pulled forward as the window goes around the camera. Hmm, I think we maybe just answered the question ourselves... :-D
I used Screen2Gif to capture the footage. It shows each frame in turn, but using that I still couldn't locate the actual frame(s) where the cuts were made. IMO, it's really well produced!
There is a ton of bonus material on the blu-ray release that discusses this in-depth, and the lengths John Lasseter and team took to ensure the portrayal was accurate and respectful of Polynesian culture. It's a really interesting watch.
Unless I'm missing something, that just looks like chromakey, with a space left in the audience for him to be imposed upon...? The angle of filming him (looking upward) increases the realism.