Playing the whole file is a strange thing - does the controller play .zip and .rar files as one unit too? In any case are you sure that you can’t just have the controller play the files that JRiver tells is exist from it’s library? JRiver, foobar2000, etc. treat an ISO like a collection of tracks, just as they do a big file with a cue sheet, a .zip file of music files or a .rar file, etc.
The DS (ignoring the bridge) has no ability to skip any of it’s input, the samples are sent without structure or feedback so the best the DS can do is to mute the samples that don’t make sense. With, say, I2S there’s not even any metadata so there’s no way to express the concept of multichannel vs. stereo, the DAC just sees a stream of samples to play.
I haven’t sent a multichannel file over S/PDIF, TOSLink or AES/EBU to see what happens, it probably sounds very weird.
The bridge is a little more complicated in that it understands how to unpack or decode a few files types (e.g. flac, mp3) but .iso isn’t among them. So once again you’ll have to present the data as a collection of tracks.
I’ve never worried about this except to not try playing a multi channel file with JRiver and all of the controller software I run (which I don’t do very often) just sees the individual tracks in the JRiver library, but I’m by no means an expert in various control point software, I much prefer browsing and playing my music directly with JRiver, foobar2000, etc.