After going to the latest version (including pull request #8 & #9) it is not possible to switch the audio track anymore. In the previous version it was possible to hold the "center button" during movie playback and then get to the default chapter and audio track selection UI of the ATV.
Now there is just no reaction anymore? Does this have something to do with the switch to the new transcoder?
The audio selection presented when holding center during playback should only show you the audio tracks in natively supported ATV video files (Direct Play media like mv4).
Anyway, all transcoded media should not show you a audio selection dialog when holding center during playback. It would be pretty awesome if this would work someday, but I guess it's more a limitation of the transcoder.
BTW this audio track selection view also would show you all available chapters and your Airplay devices. The first only for supported media like mv4.