There are algorithms in place to detect anything that sounds similar to copyrighted content. They often automatically flag covers and playthroughs, akin to a false-positive in virus detection. If the video owner refuted the flag, YouTube should have little legal basis to refuse reinstating the video.
However, there is also the argument that some playthroughs offer little difference to the original track, and are therefore too similar to the copyrighted content in question, and should therefore be flagged. For example, a guitar play-along can sound identical to the original track, so much so that the copyright can be argued to still exist.
