It's not about the site responding to DCMA requests, because how would Google know about this? This about how many DCMA requests Google gets to delist a search result I believe.
Right. What I think the parent comment is saying is that if they have contacted YouTube directly, Google (the search engine) would not get served with a take-down notice... YouTube would and it would have no influence on Google Rank.
For smaller sites, why would rights-holders bother trying to contact the site when they can just get it delisted from google?
I never mentioned smaller sites. Still, if you mean a smaller site operating like YouTube, contacting them directly would allow it to be taken off the internet rather than just out of Google results. Still, they might contact Google as well, and thus harm their rank.
Indeed. There's no incentive for rightsholders not to hedge their bets, and so even well-meaning user-generated content sites will suffer. Unless they're google properties, presumably.