What did they scan to get the eye color and lip shape?
The DNA for the eye color and skin tones, the skull for the basic features adding known statistics of tissue thicknesses over key points, and known muscle attachment points and shapes. The article acknowledges that some of the soft tissues are not unambiguously defined by the skull, most notably the corners of the eyes, tip of the nose, shape of the nostrils, and shape and fullness of the lips.
How accurate those are is a function of the skill of the person doing the reconstruction.
Forensic reconstructions of modern remains have yielded busts that vary from looking like a photograph of the now identified person, to ‘close enough’ for a loved one to recognize.
I suppose some are far enough away that they aren’t recognized at all, but the success rate is still pretty good.