I disagree with your RAW flow chart for a Nikon. The Bayer filter is an integral part of the sensor and the RAW recorded data has been influenced by the Bayer Filter. Also Nikon's NEF includes the RAW image data, the EXIF data for the camera settings and a JPEG thumbnail created from the RAW data by the imaging ASIC. If you now use Nikon's proprietary SW or SW that uses the Nikon tool kit, the stored camera settings data will be applied to the RAW data when the file is opened giving you what you saw on the back of the camera monitor. ADL also influences the RAW data by lowering exposure and moving binned data. If as you point out you use a 3rd party post processor that has not used the Nikon tool set, like any Adobe product, they cannot see the special tagged data in the NEF file, so apply their own interpretation to the Bayer Filtered RAW data.