davextreme said:

I'm going to run the film through Handbrake to watch on Apple TV.

Infinity said:

First off don't use Handbrake as that will compress the video yet another time (and possibly the audio depending on your settings). The best quality for your purposes would be from remuxing the video from the large MKV release and the DD 5.1 audio from the AVCHD release.

Unfortunately, AppleTV doesn't play well with h.264 sliced coding. It will play the video but may skip and heaven help you if you try to seek. While I fully agree that remuxing is generally a better choice, recompression is unavoidable in this case.

Don't rush to convert the v2.0 AVCHD, though; HandBrake trips over the video stream but we're looking into why.