"When you say the Camera CAN employ Nikon's scene recognition system, does that mean that this function can be switched on/off? Or is it just an inherent part of the matrix metering mode algorithm?"
As far as I know, it is an inherent part of the matrix metering mode algorithm that controls more than just exposure. I'm certainly no expert on the system, but if you are using full matrix metering the scene recognition system (SRS) is operating. It is a very complex system that affects focusing and white balance, flash, etc., as well as basic exposure. The system considers variation in color and highlight data from different regions on the RGB sensor, along with distance information from the lens (if available) comparing that information to similar data in the camera's database to try and guess what type of scene you're photographing and deliver an appropriate solution. Even if you're using manual exposure, SRS is undoubtedly still informing white balance and focus functions.
Here is an interesting interview with one of the developers of the system. It has advanced since this interview.