Do video re-encoding operations affect the container's audio file?
In ffmpeg, copy mode for -codec / -c always needs to be expressly set.

So for

ffmpeg -i in -c copy out


ffmpeg will perform automatic stream selection and copy all those streams.

For

ffmpeg -i in -c:a copy out


ffmpeg will perform automatic stream selection and copy audio stream. Video stream will be transcoded.

I suggest you read the above link on stream selection fully. It covers stream handling.