They SHOULD look different from the jpeg captured from the D50 IF Raw Shooter is ignoring the SAturation,sharpness, ect setting when it brings in the NEF files.
They'll probably look different than the jpeg images captured by the camera regardless of whether or not it was trying to use any settings. How close the output matches a camera varies by raw converter and camera. ;-)
But, if you change settings and everything else remains the same, the raw images shouldn't change if they are not using them (and I doubt RSE is using anything other than the RGB multipliers related to white balance).