How is it a false positive if there are thousands of spam links still pointing to the domain?
Usually they are correlated, not always though.
Are you saying that pages with great content typically have few spammy links? If so, the jury is out on that thesis, as many of the most popular sites have hundreds to thousands of spam sites that scrape just about everything the do & many of those scraper spam sites do link to the original source. And just by ranking for valuable keywords, over time you will likely get some spammy inbound links from sites that are scraping the Google search results.
http://www.opensiteexplorer.org/ https://www.majesticseo.com/ https://ahrefs.com/
Even once you own the domain, the links Google reports in GWT can be rather hit and miss...
I can accuse you of being a murderer but the police aren't going to arrest or ruin your (financial) life automatically.
Give me your site name and I'll give you a $5 gift, a gift that keeps giving for life with Google :) http://fiverr.com/gigs/search?utf8=%E2%9C%93&query=senuk...
Google sure loves to have all that power because it can translate it into tens of $ billions. Minus the responsibility of course because that costs money.