Admittedly, I haven't done it this way, but I think that the most recent versions of KHPRO allow for re-doing sections of the song without having to do the whole thing again.
The reason that I haven't done it this way is that trying to get a perfect "sync" is helpful to me in learning the song. (Plus, I admit, it takes more sophistication in understanding the instructions) But it certainly would come in handy, not only in doing a song originally, but if the underlying music file could be manipulated (adding more rests, etc,) then only the manipulated sections would need to be redone. Hmm... I might actually try and master this aspect.