davextreme said:

h_h, I'm going to run the film through Handbrake to watch on Apple TV. Apple TV (and Mac and iOS) don't support DTS-HD but Handbrake can convert them to AC3. Would I be better served using the soundtracks from the AVCHD since they're already Dolby Digital?

I'm not h_h, but I can answer your question. 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.