I think you over-estimate the complexity of the data being exchanged between data centres and underestimate the capabilities of these well-funded agencies that can afford top-notch PhDs, developers, engineers, mathematicians.
The article seems clear on the fact that they are able to reconstruct the data streams. It's not difficult to assume that most of the data-exchange protocols used are pretty standard or at least pretty stable, for instance Google use protobuf[1] for efficient binary exchanges, it's open source and well documented.
Data is meant to be moved efficiently between data-centres and these companies had no reason to add any obfuscation (if that was the case, they would have already used encryption). There is no reason to assume that adversaries with deep pockets would not have the technology or know-how to reverse engineer these unprotected data communication flows.
The article seems clear on the fact that they are able to reconstruct the data streams. It's not difficult to assume that most of the data-exchange protocols used are pretty standard or at least pretty stable, for instance Google use protobuf[1] for efficient binary exchanges, it's open source and well documented.
Data is meant to be moved efficiently between data-centres and these companies had no reason to add any obfuscation (if that was the case, they would have already used encryption). There is no reason to assume that adversaries with deep pockets would not have the technology or know-how to reverse engineer these unprotected data communication flows.
[1]:https://code.google.com/p/protobuf/