There are a lot of rocks beneath earth's surface, and it shouldn't be surprising or magical that some of them are heavier than others. Which does affect local gravity, especially if we talk about the rocks close enough to the surface.

Take for example a look at https://www.esa.int/ESA_Multimedia/Images/2015/04/Bouguer_gr... which has better resolution than the map in the article and tries to correct for oceans and mountains. There are clear deviations from the norm, and they are not shaped in a way that can be explained by simple rotational effects (even though those also exist)