I am NOT approaching this from any kind of racial stereotyping, but merely from a genetic point of view, but reading the article I had the same thought.

I had previously understood, that native domestic sub-Saharan Africans (i.e. those living on the continent, with clear African based heritage) did not have any Neanderthal DNA, as Neanderthals were further down the evolutionary line of the first emigration out of Africa, and were primarily European based. Therefore those with purely African genetic history would never had interbred with them.

Is this still true, or have I been walking around with a massive misunderstanding here?

As a footnote, We need to still be able to ask these questions without being afraid of the racism response. We are all different, we should embrace that and not let it affect scientific discussion or discovery.