You could probably bug MLord or Genixia to see if they can add the channel swapping as a config.ini option to Hijack. I'll bet it's just a few lines of code. Don't count on seeing it in the default player software, though. Generally, they don't waste time on features that can be corrected by properly installing the player.

By the way, have you checked to see if there's a channel-swapping feature for your head unit's aux-in? Maybe that's the source of the problem?