During the bean cut test I made the previous time, I noticed darkening on parts of majority of the beans. Beans in questions have 30 percent dark region. I thought it was natural so I just let it go.
Then while sorting beans for the next roasting batch, I spotted one bean with a severely darkened side. If I never know better, I will immediately think that it was already roasted and accidentally included here. The darkened side was partly shelled.
So the darkening that I noticed before was not natural. It is a sort of process abnormality that may or may not affect product end quality.
Thanks to amanochocolate.com which has a nice detailed explanation on fermentation. During the process, if the beans are turned too frequently, the beans get more oxygen exposure. Then, resulting to too hot temperature and darkening. On the contrary, too infrequent rotation will result in uneven fermentation.
They never mentioned how much rotation is enough though, nor discussed the effect of bean darkening.
As far as roasted bean flavor is concerned, every bean from the same batch has slightly different taste. Some are neutral and some are good, others are bad. There are few that exhibits exquisite flavor. If I only have the way to sort beans according to flavor, I surely do it.
One acquaintance who happened to be in cacao farming told me that different nibs color pertains to specific varieties. Cocoa farmers tend to raise mixed species for number of reasons. Darker nib color may also native to specific variety and not just a result of improper fermentation.