well so i guess the question is, what is your goal?
if you are going to calibrate your frames then you should not debayer them with DSLR_RAW. you should set it for raw CFA or raw RGB.
if you just want to load an image and look at the debayered result, you can set up DSLR_RAW to debayer the image, as you have.
you can also use the debayer process to debayer one of the images when opened as raw CFA or raw RGB.
i don't have a nikon camera. it's possible there is a bug here where DSLR_RAW can not properly debayer a .nef file. i kind of doubt it, but i can't test it either.