Apple released tvOS 9.1 today, which seems to have fixed the issue of the 5.1 audio tracks not automatically being selected on the Apple TV. It works differently than previous generations though, and doesn't show you both tracks in the audio menu. Instead it works just like it's set, so you only see one track in the audio options.
The patch also fixed an issue where the Apple TV would not trigger Dolby Pro Logic Playback with the ‘Settings > Audio and Video > Surround Sound’ option set to 'Dolby Surround'. It now automatically switches between Pro Logic and Dolby Digital based on the audio track just like it did in previous generation models.
