Other than the material used for the different colors, most of the time it's just product placement. The marketing would look at which is their more popular models and create value for those to maximise profit. I assume black dial for Rolex is their more popular variants.
For example, when Apple first started their Black MacBook series the price was higher because it was a new 'product' in their range and everybody wants one. Technically speaking white pigments are more expensive because you need special additives to reduce the white from turning yellow prematurely.
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