I still don't understand why Google went on the route of proactively removing content rather than reactively.
Content ID was born out of a desire to keep Viacom happy after Google got sued: https://en.wikipedia.org/wiki/Viacom_International_Inc._v._Y...
In short, it's not YouTube's (or GitHub's, etc) call, this is part of the agreement with copyright holders (the DMCA copyright law).
Don't take that as an endorsement though, I hate the system as much as you do.