Whatever the recording, audio just wants to be heard: the trick is picking a shape that plays where you need it. It was born in wherever your microphone, DAW or download came from, and its real weak spot is nothing in particular; the limits belong to whichever format it happens to be wearing.
MKV is the format that hoards: video, a dozen audio tracks and every subtitle, all in one box. The Matroska container: it will hold practically any codec ever made. That makes it the right destination when what you need is high-quality rips and archives with multiple audio and subtitle tracks.