Sometimes you simply want poly wave files: surround recording or phase coherence safety.
Mono files can slip in time accidentally during edit.
I record surround material in mono files, save and work with those, and export to multi-channel FLAC files.
A few more practical reasons I do it that way- my channel assignments into the recorder are not usually arranged in standard order, so I rename the raw files with the appropriate channel indicated in their file name, FLAC and archive them. Then when I get around to working on them I bring those into my editing software and time-lock them together so they can't be slipped out of sync accidentally, work on the project, then export multi-channel WAV or FLAC. Keeping them as individual files makes it easier to substitute alternate channels if I recorded them, preview the files with most any media player, and copy single channel files or pairs out for other use. For instance, I can just pull out the Left & Right Channels.