Just did a quick check on the South Indian uncle-niece marriages. It is found among South Indian Muslims (see Genetic Disorders of the Indian Subcontinent, ISBN 978-1402012150, Springer). It is also found among Indonesian Muslims, the nation with world's largest Islamic population. I do not believe this means we should insert uncle-niece back in somewhere, because 4:23 verse indeed forbids it. This needs a lot more study.

Ozziegt, the references cited in the article offer abundant specifics and discussions on consanguineous cousin marriages of women in Islam. Let me think a bit more on how to best address your "applies to both" concern.