"Remember folks! Don't use SEO! You're subverting das Googlebot!"
But play by all their algorithmic rules, or you may be randomly penalized.
This is called a False Positive. It's Google's fault, not the legitimate domain owner's. This is a hard problem(tm) for sure, but not an excuse.
The fact of the matter is that someone is always unhappy when it comes to spam control. If the restraints are too loose then suddenly everyone is screaming about how "spammers are ruining Google" and "Google is doomed because of spam" (this was very true right before the Panda rollout). However, if Google starts to crack down, then you get more false positives and more people upset for different reasons.
Unfortunately, no pattern recognition system runs at 100%. That's not a hard problem(tm), that's an impossibility. Relatedly, I don't really see what's wrong with assiging a "reputation" to a domain name. As the article states, it's possible to climb back up to "good" status, it just takes some extra work. Kind of like in real life.
My point is that Google suggesting you register a different domain because their href-based reputation sucks over time is a cop-out. This specifically falls under the "Things that are Google's fault".
Matt's suggestion here is definitely practical, but it's a fault in how Google looks at domain reputation. When he talks about "having to renovate a domain" he's talking about you the consumer of a domain legally acquired and without spammy content hosted on it, having to play Google's algorithm, because their definition of "spam" is absolutely massive, vaguely defined, and with way too long of a ttl.
And with a massive, undefined, long term concept of spam, you're going to have ridiculous FPs. Which Google has, and is now recommending is somehow your responsibility.
This is entirely their fault, and it has to do with how they are determining reputation, not that they have reputation at all.
How is that behavior any less "bait-n-switch" (or influenced by money) than buying a site or renting some links?
We've just been lucky enough they're looking at profit on a long enough time scale that loyalty through product quality is a metric they've thought about.
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.