Rob, Richard,
<<If one changes the profile for the input RGB colorspace in the
Preferences, doesn't this override the Color Mode setting for NEF files
in the Advanced RAW palatte?>>
No, as I understand it, it works like this: The Color Mode controls
the rendering or "look", not the encoding or "color space". On the other hand,
the input RGB colorspace in the Preferences changes the encoding but not the
rendering. Changing the rendering doesn't change the encoding and vice
versa.This means you can mix and match renderings and encodings. For example, if
you like Mode 1a rendering but you want the wide gamut of the ProPhotoRGB
encoding, you can have it.
<<Is the NEF first converted to the color space
noted in the
Color Mode setting, and then converted to the color space
in the Color
Management RGB preference on output, when a file is saved?>>
No, as I understand it, its the other way around. On open it first encodes
based on the Preferences and it then renders based on Mode.
I have struggled with this myself and I agree with you that it is
confusing.