With MKV2M4V app, the source’s video is always copied to the target regardless of the audio options. But if the target container (m4v, mp4 or mov) doesn’t support this video codec, it will be failed.
Audio Preset: Mac, iOS Device, Apple TV
(Audio Preset) - (Target's Audio Codec)
’Mac’ - ALAC
‘iOS Device’ - AAC/160Kbps
‘Apple TV’ - AC3/640Kbps and AAC/320Kbps
In these three options, basically, the source’s audio will be converted to the each codec as the above. And it can select only one track from the source’s audio.
But if the source and target audio codec are the same, the source’s audio will be just copied in order to shorten the conversion time, it isn’t converted. That is, it will be worked as 'Pass-through'.
Audio Preset: Custom
On the other hand, in ’Custom’ option, it will always work as the chosen audio codec option. That is, this option can do things that it is converted to the same audio codec.
And it can select two tracks from the source’s audio.
All ‘Audio Preset’ options
If it is worked as ‘Pass-through’ and the target container (m4v, mp4 or mov) doesn’t support the source’s audio codec, it will be failed too.