Agree with your suggestion and there is probably a 'version 2' of the product option domain. Some parts of it (like what you mentioned) could probably be improved.
However, as a workaround you could do exactly what you suggested and just remove Skus that have the 'red' product option value. Then you could override our ProductOptionsProcessor to instead show only the product options that have Skus mapped for that particular set of Product Option Values.
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