My guess is that they're doing it through ML. The old "cancel out the left track with the inverted right track" trick is probably good enough, but I don't see why Apple wouldn't take it one step further.
> Do any audio file formats support separate tracks with level info?
I don't know what file format audio engineering software uses to store all the track info but my guess is that it's akin to a zip file containing a flac for each track.