There are two different types of noise reduction in most cameras:
- High Iso or standard Noise Reduction: Applied after the image is taken, similar to what you can do in post processing and it does not affect the RAW file.
- Long Exposure Noise Reduction (LENR): The method you referred in the OP where a dark exposure is made and then substracted to the image. This does affect the RAW file, since the camera performs the substraction of the image and dark frame before recording the raw file.
The inconvenience of this method is that for every image you take, the camera records a dark frame, doubling the time it takes to have the camera ready for the next image.
One option to overcome this is to capture a dark frame separately and then do the substraction in post. The dark frame shoud be taken with the same ISO and exposure time as your image.
The issue here is that popular raw converters such as LR or C1, do not have the option to handle the dark frames, and you are left with less user-friendly applications such as RawTherapee, DCRaw or astrophotography programs. Some people perform the substraction in photoshop but it is not technically correct, unless you develop you raws using a linear profile.