The author is also picking quotes from different programs and mashing them together to come up with their speculation. Note how the commercial entities are discussed under the "Sentry Owl" program on page 7, but the "covert or under cover" quote comes from the "Sentry Osprey" section on the last page, which appears to be talking about the NSA working with the CIA. If NSA employees were working with the CIA on anything outside the US, it would make sense that they'd be undercover. Maybe they are infiltrating companies, but the source document doesn't support that assertion.
Schneier isn't name-dropped at all in the article. I find it odd that they would quote Matt Green and Chris Soghoian by name, but mix in the opinions of someone as well-known as Bruce Schneier without mentioning his name anywhere.
Bruce Schneier was given an opportunity to meet and review a large collection of documents but yes its true we don't really know.
There's a Chinese whispers effect to all this where vague assertions are repeated over and over until they become considered definite facts.
"...by exploiting inherent weaknesses in Facebook's security model." - GCHQ
That's Facebook. The Yahoo and Google stuff has been very widely reported and are direct from Greenwald and the Snowden leaks. Other links (in particular the PKH link) contain other information.