I actually just mapped it out in my business ideas note folder and yeah. I don’t see how you can build a decent tool for this job without having copies of the actual waveforms requiring some form of commercial license, however it would not need to be a performance license which seems to be the thing the publishers are most familiar licensing. So I’m not sure if this would make the process easier or harder but I definitely don’t see how they can argue the rights to use but not play the music are more valuable so they should in theory be cheaper than the sort of price iTunes and Spotify are paying per track.
It should be part of the YouTube post-upload processing. You find another YouTube link of the offending music, it syncs the two audio tracks, and removes from your upload.