Exactly -- and the situation arises because "fair use" determinations aren't scalable. It literally ultimately takes a court and a jury to determine if something is fair use or not, which is incredibly expensive.
Now in 99.999+% of individual human situations, it never gets that far because it's pretty clear to a person in advance whether something is fair use or not, or they ask a lawyer and assess the risks, etc.
But when you're dealing with user media at scale, that system falls apart. YouTube can't have a human lawyer manually review each clip for fair use, YouTube certainly can't trust uploaders because there are tons of people trying to upload entire Hollywood movies, and asking copyright owners to manually review each flagged match is similarly not scalable.
So YouTube simply implements a content matching system that disallows more than a certain amount of copyrighted material period. There's no other scalable solution given existing copyright law.
And honestly, this new eraser tool is a really good solution if it works. If it can simply and effectively remove unwanted background music that was never wanted/intended to begin with, then it works for everyone -- pirated content uploads are still blocked scalably as well as unlicensed sountracks on webisodes etc., but people can still upload personal clips and instead of them being blocked, they can just remove the music instead.