According to ChatGPT, the eye color and skin color were determined using DNA analysis, and represent approximations. The sister with darker hair likely had slightly darker skin as well, representing genetic diversity in ancient Europe. The two sisters would be more closely related to the Sami or Basque people, than most modern Europeans- but only distantly so.
Cheddar Man had dark skin but blue eyes, but he was mesolithic, not neolithic, and lived about 10,000 years ago. Quite a bit older.
People of European ancestry can have alot of physical variation, even among family. My brother has skin that is a full shade lighter than mine, red hair, and blue eyes, whereas I have dark brown hair, brown eyes, and almost a Mediterranean complexion.
Speculations in the article about the nature of the sisters work and deaths are also logical, if speculative. Alot of ancient cultures practiced slavery and forced labor, for all sorts of reasons. They also had ritual human sacrifices on occasion (though some writers, such as Greeks or Romans, had reasons to embellish or misunderstand such accounts), so it's not out of question as an explanation. Mines in particular were places of magical enchantment, liminal spaces that connected to unseen worlds, often full of creatures that guarded them and didn't take kindly to intruders (hence European stories of kobolds, goblins, and other spirits that guarded liminal spaces such as caves and mines).