Whitey - 3:58 am on May 18, 2013 (gmt 0)
The problem is that nobody knows what links these notices are specifically referring to. Take this BBC example, where an employee questioned the notice, and John Mueller from Google responded :
Google's John Mueller dug into the details and discovered this was a "granular" penalty. John said in the Google Webmaster Help thread:
"Looking into the details here, what happened was that we found unnatural links to an individual article, and took a granular action based on that. This is not negatively affecting the rest of your website on a whole." [seroundtable.com...]
The consequences of Google being vague is that it causes the webmaster to be on guard and take action on all links considered "unnatural" , as at the same time Google likely cannot fully detect all "unnatural links". On top of that Google improves it's data footprint of what is likely to be "unnatural" links via subsequent disavow tool activity, plus provides a widely publicised FUD warning to the SEO community about paid and SPAM links.
But for the site-owner, what if some of the links are undetected or perhaps wrongly interpreted as "unnatural", and removed, causing the site's rankings to bomb by widespread removal?
Some major brand sites I know of did this, and their rankings went rapidly south. It became a can of worms to fix.
With the Penguin 2.0 update coming, webmasters will have the opportunity to reflect better on what they should have done. It may be too late for some to apply a remedy without getting hit in this next update.