I think this is the reason YouTube is complaining. Previously they just got away with Content ID and it was just how the service worked. Now the law is drawing

I think this is the reason YouTube is complaining. Previously they just got away with Content ID and it was just how the service worked. Now the law is drawing attention to the concept and people might get the idea that maybe an automated decision isn't the fairest implementation of this law and not having a real appeals process is unacceptable. Especially if you consider that the EU already explicitly included a ban of purely automated decisions in the GPDR (though "luckily" that is probably not applicable in the context of Article 13, yet). YouTube doesn't protest the idea of upload filters. YouTube just doesn't want upload filters to be a thing so much that they might end up being regulated and have legal decisions based around them because that means Content ID will be regulated and have legal decisions based around it.