It looks as though a valid entry in an M3U playlist could be a another playlist, allowing playlists to be 'chained'. What if the content of that other playlist was just a .CFG file - let's call that other playlist a 'config playlist' for the sake of argument. Rockbox could then 'play' that config file, as suggested above, when it encounters the config playlist. Other players, eg winamp, would just ignore the config playlist if it did not exist on the PC, but should not discard such an entry when editing (because it is a valid entry).
On the iriver you would simply need a few one-line config playlists that 'wrap' your different config files. This might still cause a problem if the iriver is just being used as a hard disk for Winamp, because then Winamp would find those config playlists and cause some sort of error.