"While Google have ever publicly disclosed how Content ID works, the technology is actually licensed from a company called Audible Magic: http://www.audiblemagic.com/ - essentially the technology works similar to that of major music finding apps like Shazzam or Soundhound. "
from https://www.quora.com/Does-Content-ID-look-for-a-match-of-the-actual-code-or-a-match-of-the-audio-produced-by-the-code
But check all the hard work done by Scott Smitelli in his "Fun with YouTube’s Audio Content ID System":
http://www.scottsmitelli.com/articles/youtube-audio-content-id
This is from 2009, but if still applicable, shows you can outwit YouTube by using Audacity to alter the music speed or pitch by 6% in either direction or knocking the song out of phase.
It's not clear what would happen if, instead, you inserted tiny gaps of silence in the unadulterated recording, a la Cinevia for films, or reversed only a handful of small unimportant music slivers, a la the end of 'Strawberry Fields Forever'.