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I think a "digital ND filter" could be accomplished by attenuating the sensor analogue output before it's converted A-to-D. This implies that there's at least slightly more dynamic range in the sensor analogue output than in its "matched" AtoD converter, but this is certainly possible. A pre-sampling method for "lowering ISO" could provide effectively the same results as a physical ND filter, but only if it's acccomplished before the RAW file is created (i.e. before the sensor analogue output is sampled and converted to digital). Of course, this would also require super signal-to-noise performance.
The charge storage ("well") is the bottleneck at the lowest ISO for all sensors I know. It is possible to lower the ISO sensitvity by attenuating the signal electrically between the photodiode and the charge storage. It would have the benefit of getting a very low photon shot noise and a very clean image, since all the photons are converted (as opposed to a physical ND filter where the photons are converted to heat in the filter). On the other hand, it would increase the read noise and higher ISO will suffer. If this method is applied, it would however be no reason not to make this available simply as lower ISO.
Since RAW often has more highlight headroom than JPG, it is reasonable to ask if the ND filter is just eating the headroom. This would be feasible up to about 1 stop, but hardly 3 stops. But again, it would be better to make this available simply as lower ISO, like ISO 50 in Canon DSLRs.