What do the pros do? (or: Scene Mode)

I agree, nothing here should bug you.  It should be seen as an added benefit of the Nikon that you can choose to use or ignore.  I do agree with your sentiment, though, that a straight forward tool has its appeal.  Although, some digital cameras have more going on behind the scenes than others, they all need to cook, or post process, the RAW file in order to create the JPG.  Without knowing more, I suspect, along with others, that it is the post processing that the D600 is doing (in the scene mode) that creates the look you like.  If you don't want the camera to do it, you can do it yourself on a computer.  LR will take you quite far, but something like Photoshop will be required for certain types of edits.  Oh, and don't think that post processing is not old school or not for the purist, as professional photographers in the film era would do a significant amount of it (in a darkroom, rather than with Lightroom).  In the digital post processing world, the tools are different, but the goals are often the same.

See Ansel Adams' Moonrise, Hernandez: http://rcodaphotography.blogspot.com/2010/01/inspirations-24-moonrise.html

(Comment not meant to start a film vs. digital or PP vs. SOOC debate)