Ian,
Is the jpeg that I extract in PM different from one obtained by saving a NEF as a jpeg in Nikon Capture NX?
Most definitely. The JPEG that gets extracted from a NEF is the JPEG that was inserted by the camera. On the other hand, if you save your adjusted NEF in NX as a NEF, then NX puts a new JPEG inside the adjusted NEF. If you extract that JPEG, then it is going to be very similar to the JPEG that NX would create.
I hope this is clear?
-Kirk