The phrase “baffled” in the popular headline overstates the researchers’ position somewhat.

They are not baffled; they are appropriately cautious about interpretation in the absence of written records or direct comparative evidence.

The evidence is clear.

The meaning of that evidence is contested in exactly the way that honest archaeological interpretation should be.

The term “scooped out” in the headline is a popularization of the more precise description in the paper: “breakage of the cranial base and internal cutmarks are suggestive of deliberate removal of the brain.” The physical process was probably more methodical and less dramatic than “scooped out” implies, but the essential claim — that the brain was deliberately removed — is consistent with the published evidence.

The claim that the bones were “turned into tools” is accurate but requires the context that the modified bones were subsequently returned to the burial in anatomical position — a detail that significantly affects the interpretation and that was not always prominent in popular coverage.