To answer your question though, end-to-end encryption of data in transit will obviously interfere with an employer's ability to log transactions.

I think Mr. Baker's arguments were more directed at the recent ubiquitous iPhone encryption controversy (in fact, after doing a quick search, he made almost the exact same argument in the NY Times directed explicitly towards Apple[1], although I think his wording could be toned down slightly). Since the decryption mechanism on the iPhone is tied to chip inside it, it limits a company's ability to hand you a corporate iPhone and still be able to monitor what you're doing with it, hand it over to the cops, etc.

Baker makes the further argument that while Apple can encrypt everyone's data to the chagrin of the FBI and the federal government is unlikely to enact any laws preventing it or hindering sales, Apple will have a much harder time doing the same in certain foreign markets. A country like China will likely have much more political will to push Apple out of the market if their cops can't decrypt people's phones. Maybe that will ultimately be a good thing, but by trying to send a message to the US government they might be opening up a much larger can of worms overseas.

[1] http://www.nytimes.com/roomfordebate/2014/09/30/apple-vs-the...