Re: One thing that people seem to be missing
That's how both Adblock Plus and Adblock work now, the adblockers use a separate whitelist. But it's not hidden at all, it's here https://easylist-downloads.adblockplus.org/exceptionrules.txt (don't be surprised, there are a lot of domain grabbers, toolbar vendors or link farms in this list. Eyeo is not picky with the choice of the companies in this list, they just care if the ad itself is "acceptable".
This whitelist automatically overrides the filter rules of *all* blacklists, whether it's EasyList, ABPindo list, Fanboy's Ultimate Block List, etc. inside Adblock, Adblocks Plus and Crystal (iOS). The most popular filter list is EasyList, which is also (mostly) hosted on the servers of Eyeo https://easylist-downloads.adblockplus.org/easylist.txt (they simply offer the fastest connections, that's why most of the other adblockers include this URL, too, by default).
It's also an open secret that a few - at least one where we know the real name - of Eyeo's employees maintain both the easylist and the whitelist. But, to make that clear at this point, we have *no* evidence that the Easylist contains any filters to led ads through. Nevertheless you're totally right when you write that it's at least alarming and has to be monitored that both lists are hosted (and partly maintained) by the same company. A company that controls the two most popular adblockers with approx. 100 million users.