Your article discusses skin color.
Skin color cannot be deduced from skull shapes. However, DNA can determine eye color, hair color, and I think also skin color. That is, if DNA still exists.
Modern methods of extracting DNA are more successful than techniques a few years ago.
Scientists believe that modern mankind began in Africa and traveled north to the rest of Eurasia. It is possible that humans were dark skinned originally, and that might explain why Africans, today, are dark skinned. Also, if mankind is related to bonobo chimps, and chimp's skin is black, it stands to reason that early man was black.
Through DNA, we know that Neanderthal skin was white, and their eyes were light (typically blue), and their hair was blond or red.
We also know that modern man has as much as 6% neanderthal DNA. There are no existing Neanderthal male lines, nor female lines, but the DNA exists in mixed lines. For example, your grandfather's y-DNA is passed to male kids, but fails to get passed to female kids. Yet, the females have DNA that is not y-DNA from your grandfather.
It is possible that Neanderthals, who left Africa much earlier than modern mankind, could have had sufficient time to evolve lighter skin. This would enhance their body's ability to absorb more sunlight from northern sun (which is less intense because it penetrates more atmosphere. This sunlight allowed their bodies to metabolically produce vitamin D. They would also blend in with snowy country.
Could it be that the blonds who exist today could be blond from their Neanderthal DNA? The prevalence of Neanderthal DNA seems higher in countries with blonder people.
Blacks didn't breed with Neanderthals, because the Neanderthals had left Africa long ago.
As for refining facial features without artistic biases. The science of facial reconstruction is getting more exact. However, as your article points out, there is a difference in the muscle of apes and humans, and, unless DNA is used it is an artist's guess about the type of muscle.
As we learn more, we leave less to chance, and eventually form a much clearly picture of ancient man and ancient artifacts.
Many criticize scientists for being racist for trying to determine such things as skin color and eye color. Yet, pure science doesn't seem to preoccupy itself with such concepts except to attempt to get as accurate as possible to reality.