If Nikon - or anyone else - are scaling raw channels, that is quite unfortunate, and - err - dumb.
That doesn't require one doing it in the Raw file data. It could even better be postponed to a more potent processing environment which can also use more bits.
While scaling Real Numbers is linear, scaling finite precision numbers is not.
To illustrate the problem, consider a 3-bit RAW camera, so the RAW format supports values 0-7, but where the sensor red channel is usually in the range 0-5. Let's try scaling the red range up to 0-7 and rounding to 3-bits.
Oh dear. The input has even steps, but the output doesn't.
Also, we have a problem if we take a picture where the sensor red channel goes up to 6.
If you have some very clever RAW conversion software that analyses the gaps in the RAW red histogram, in principle, that software could undo the damage done by scaling and rounding back to 0-5 - on the basis that a histogram with regularly spaced gaps in it was statistically implausible.
OTOH, if your RAW software takes this scaled RAW data at face value, the non-linearity introduced by the scaling may introduce banding in the shadows, and emphasise sensor pattern noise in the shadows, which might not otherwise be visible.
If the manufacturers want to offer more ISO settings than their hardware has gain settings, the way to do it is to record the requested gain in the metadata, rather than by attempting to scale the "RAW" component values.