Is there any effect/benefit of adjusting Picture Control other than for the out of camera jpegs?
Yes, as noted Capture NX-D and NX Studio apply the in camera Picture Control settings to NEF when opened. Also modified Picture Controls can be saved in camera and in software. Then there is Nikon Picture Control Utility 2 installed with CNX-D and NX S. In PC Utility 2 you can create your own custom Picture Controls and you can add custom curves to your custom PC. Those PC(s) can be installed in your camera and in CNX-D and NX S. The picture control system is quite useful if one uses Nikon software to develop NEF files.
I normally shoot with Auto PC and then switch to Standard or Neutral PC in Capture NX-D. In extreme situations I’ll use the Flat Picture Control. If I understand correctly Flat is primarily intended for Video. I’ll switch to NX Studio when Nikon rolls out a few bug fixes disguised as upgrades.
Capture NX-D can "Save all adjustments" in an *.NXD file and NX Studio does the same with *.NKA files. Unfortunately NX Studio does not read *.NXD files from CNX-D just as CNX-D didn't read the adjustments save in NEF files by Capture NX2. Currently the only bridge between *.NXD files and NX Studio is a clumsy use of both CNX-D and NX S when the adjustments are saved in the *.NKSC (Side Car) files. To save the *.NKSC (side car) file switch to a different NEF file or close CNX-D.
Anyway Picture Controls are useful to Capture NX-D and NX Studio when developing NEF(s) and I think they were to Capture NX2 but it's been a long time since I used Capture NX2.
Best,
Dave