The theory behind that statement in the manual is that Matrix Metering uses a set of pre-defined algorithms to assess the distribution of brightness across the frame and allocate exposure accordingly. As such, the metering system is already "compensating" for what it sees as unusual lighting (for example, a subject in shadow in front of a bright background), and applying compensation manually for all shots without thinking about it can sometimes result in inappropriate exposure.
Centre-Weighted and Spot Metering don't employ the same "intelligent" assessment of the scene, so the risk of "double compensation" is reduced or eliminated.
Having said all that, I regularly use Exposure Compensation with Matrix, but only on some shots - when experience with the camera suggests the scene is such that Matrix may not expose it to my liking.
If your D700 consistently overexposes EVERY scene when using Matrix Metering (rather than simply not matching your preferences), there is probably something else wrong that could be adjusted by a service agent.