How about this newer article [1], also by Ambinder, which the top post in your link links to? It seems to be speculation but it's the best reconciliation that I've seen of the leaked document and the denials of the tech companies. I also find it to be plausible, overall, if a little too trusting of the NSA's auditors and methods.

http://theweek.com/article/index/245360/solving-the-mystery-...