This is an often misunderstood issue.
A base ISO 200 verses 100 is GOOD, not bad, in most fundamental ways. It means the sensor is more sensitive and, all other things equal, should deliver better high iso performance. It can develop a full exposure with half the light. That is a good thing.
I think Nikon put the ISO 100 "cut" in there to please numbers measurebators ("what? No ISO 100?), and as a convenience feature to allow fast lenses to be shot wide open without adding ND filters. And, of course, other recent models "support" this, for better or worse and it is a perceived benefit. That is more marketing than technological need.
Each time you double (or increase at any level) the output of the sensor, you add more noise. ISO 800 has to be doubled twice from base ISO 200, but THREE TIMES from base ISO1 100.
Having the ISO 100 "cut" saves you the trouble of mounting a 1 stop ND filter. That's all it does (most likely, but a good speculation).
A base ISO 400 would be even better, indicating an even more senstive sensor. You then have issues, of course, shooting fast lenses wide open in bright light, but everything is a double edged sword. A base 400 sensor only has to be doubled twice to get to ISO 1600.
In the film days, low ISO was "good" because low ISO film was finer grained. In digital terms, it would be like varying the number of pixels based on your ISO setting. People put up with low ISO slide film to get the fine grain detail (and other attributes). The low ISO rating was not, in itself, a benefit for anyone other than masochists, especially shooting handheld. We put up with it to get fine grain, not because we liked long shutter speeds (in most cases- there are exceptions like shooting waterfalls, I guess)
This is still true in a digital sense, to the extent that low res sensors are less noisy than high res sensors, but within a single body, for a given sensor, higher ISO for a given res/noise level is GOOD, not bad. If Ektachrome 200 had the same resolution and small grain size as Ektachrome 25, no one would ever have shot Ekt 25.
Does that make sense?
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Regards,
Neil