Differences between African groups being bigger than between blacks and whites in NA don't make the rough categorization no longer work. For example, there's rather little genetic variety within dogs, or between dogs and wolves, but that doesn't say much about how impactful the variation is: Chihuahuas and Huskies are genetically really similar to each other, but no one in their right minds would disagree that you can comfortably put them in different, very real, very genetics-based buckets.

In general, arguments of variation within a group are not arguments against considering between-group differences, or those between-group differences being real. The variation within a category cannot be dismissed, though, it's hugely important for understanding the world properly and for guiding personal conduct.