I'm the opposite of an Apple Fanboi, but I doubt that this happened at all, or as the magazine is reporting. I would suspect Apple marketing maintains a blacklist of reporters and publications they don't invite to events, and I'm sure they just add people to that list, likely without notifying them they've been added. What would Apple have to gain by telling a publication they've been blacklisted.
Suppose the iPhone 6 Plus really has a major design flaw. What can Apple do about it? Retire the phone? What would it cost to them? Impossible.
They just have to stop the rumor, pretend it's not true, keep it quiet. So pretend it's not frequent, that only 9 phones were reported malfunctioning. They're the one who have the stats of reclamations: 9 or 900, no one can provide a number with better credibility. And stop the media from talking about it.
Apple make the magazines fear to be excluded, just like what happened with Gizmodo. On the contrary, do the magazine really have something to gain by pretending they've been blacklisted, if it's not true?
I completely agree with you that Apple is likely lying about numbers or trying to make this a non-issue. What does the magazine have to gain? They made you look.