It looks pretty speculative to me. Directly from this article: "The most controversial revelation in Sentry Eagle might be a fleeting reference to the NSA infiltrating clandestine agents into “commercial entities.”", "It is not clear whether these “commercial entities” are American or foreign or both." and "The document makes no other reference to NSA agents working under cover. It is not clear whether they might be working as full-time employees at the “commercial entities,” or whether they are visiting commercial facilities under false pretenses."

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.