What affect will the in camera settings have on a jpeg file? Same as a raw file? I know a raw file can be processed where a jpeg is essentially processed in camera. So…adjusting the in camera setting will have no affect on a raw file?
The settings used in camera do have an effect on the RAW or NEF file. There is a JPG preview included in the NEF file. That preview is the same as a JPG file that can be saved in camera as a standalone JPG.
The NEF file will be tagged with the in camera settings and that will be your starting point when you use Nikon software, CaptureNX2 or CaptureNX-D. You can change those settings before you develop the NEF as they are not "baked in" so you can develop the NEF with other settings.
Third party software may or may not be aware of the incamera settings beyond a few like the white balance settings. The don't have Nikon's secret sauce so they can't develope the NEF exactly as Nikon software would but the have their own secret sauce. It like to different cooks creating the same dish, similar but different.
I like Nikon's CaptureNX-D though it sucked at first. I liked Nikon's CaptureNX2 and wished there had been a CaptureNX3 but that was not to be. I recommend downloading CaptureNX-D and giving it a try. It's a free download. I develop my NEF(s) in CaptureNX-D and pass them to Photoshop for finishing.
There are may alternatives to Nikon software from Capture One, DXO, Adobe and more. I want to try Capture One but haven't made the time yet.
I hope something here helps,
Dave Hartman