It seems to me that you are focusing your attention more on the simplified graphics used by the science editor of a newspaper to popularize the scientific findings of the study than the results of the study itself. As I understand the project, the investigators developed a new technique for extracting valid human dna from mummies, and tried it out on a fairly large sample of mummies (150 or so) and were able to extract some usable dna information from about 100 (but only complete information from three). The results were entered into a genetic database for this project and compared to other existing genetic databases.
The fundamental comparison made was between a modern sample, living in Egypt, and three subgroups of ancients, from different time periods, drawn from the mummies. Findings suggested that all the subgroups differed from the modern sample. The modern sample had significantly more genetic factors from sub Saharan regions of Africa.
I think you'll get a much better understanding of what the investigators found if you read the scientific article:
You might find this quote from the study especially interesting:
However, we note that all our genetic data were obtained from a single site in Middle Egypt and may not be representative for all of ancient Egypt. It is possible that populations in the south of Egypt were more closely related to those of Nubia and had a higher sub-Saharan genetic component, in which case the argument for an influx of sub-Saharan ancestries after the Roman Period might only be partially valid and have to be nuanced. Throughout Pharaonic history there was intense interaction between Egypt and Nubia, ranging from trade to conquest and colonialism, and there is compelling evidence for ethnic complexity within households with Egyptian men marrying Nubian women and vice versa51,52,53. Clearly, more genetic studies on ancient human remains from southern Egypt and Sudan are needed before apodictic statements can be made.