I think the aggregate of all "toxic link" reports cover 100% of a site's links. John's right, they're hilariously bad. My teams' SOPs have been "only deliberate schemes" ... if there was an obvious webspam footprint to something extra spammy that somebody did, since that's long been the spirit of how Google fights spam algorithmically. Or a clear negative SEO attack... super obvious when that happens, often 10K new links overnight with pornographic anchors.
I don't know what to think of the tool anymore, but we'll still use it narrowly for good measure. John's downplaying the value, but saying that it works the same as ever? Does he mean that it was always the equivalent of those disconnected "door close" buttons on some elevators? @Cyrus Shepard did an experiment where he disavowed all his links and nothing happened, but it's unclear if that's because the tool is bunk, or he hit some "measures to save you from yourself" that Google mentions often.