It's important to start with this: in-camera generated JPEGs are also software-generated. They're just generated on a small embedded computer with a lot less processing power than a laptop or desktop system — which generally means specially-tuned chips hard-coded to do specific operations quickly. Combine that with a much more limited user interface, and that means that the conversion is generally a lot less flexible — but doesn't necessarily mean that it's worse.
In this case, it seems that the in-camera software does a better job at a particular thing you care about than the desktop computer software Nikon has provided. You're right that generally this software is tuned to give similar results to in-camera processing, but the specifics can (and do) differ, especially when you look really closely.
In fact, the camera manufacturers put a lot of effort into making in-camera JPEGs look really good, with a lot of work on color tone curves (sometimes "film simulations"). If getting that result is what you want, you're right — there's no point in RAW in that case. Well, at least mostly; RAW also protects you against mistakes like incorrect white balance, and can help with over- or underexposure, but you can get that by saving as RAW and converting to JPEG manually in camera, adjusting parameters after the fact.
RAW on the desktop really shines when you want something different. Since you have that RAW file, you're not limited to Capture NX-D. You can try Rawtherapee or Darktable (both free and open source software), or Lightroom, or any of a number of other RAW conversion programs. You can tune chromatic aberration correction in a lot of different ways in all of these different programs, and apply any tone curve you like — and if you change your mind, no problem.