Even if the sites are not relevant, the existence of a link does not mean the site which the link points at was responsible for creating the link. In some cases (especially with website hacking) those who create the spam will link to innocent third parties to create a smokescreen. Google can & does burn some of these "drive by shooting" sites to a crisp.

Check the people who try to drop profile links & comment spam links on your blog and such. Are there any websites which have as many spammy inbound links as YouTube does? How many people does Google allocate to cleaning up YouTube's spammy link profile?

There's another factor in that Google may shift what is considered reasonable over time. A buddy of mine got an unnatural link warning where the link cited was a link that has been in place LONGER THAN GOOGLE HAS EXISTED.

Now consider that some websites are bought & sold, change ownership, etc. ... does it make sense to penalize today for something which happened 10 or 15 years ago?

Another factor is that just by ranking you will pick up some scraper site inbound links you do not want. Many of those sites in various forms or fashion are monetized via Google ads. Google continues to run their ads on many of those aggregation sites, yet you may get an unnatural link penalty for having links from the same sites.

Good enough for Google, NOT good enough for you TM