From the article: "initial theories suggested they were used as territorial markers for ancestral grazing grounds. Yet, as more and more were found, all dating to the same period, a different understanding emerged."
So the cult idea wasn't the archeologists' default description and their initial ideas were the same as yours. There aren't many hints in the article on why they revised that idea, but the following paragraph says this: "They've uncovered large numbers of cattle, goat and wild gazelle skulls and horns in small chambers in the heads of the mustatil, but found no indication that these were kept for domestic use. Since no other animal's body parts were found, it led the team to deduce that these were sacrificial. It further suggested that the animals were sacrificed elsewhere. This is important because it is evidence of a highly organised, cultic society, much earlier than was previously thought – predating Islam in the region by 6,000 years." Any theory will need to explain away the piling of animal skulls, and absence of the rest of the animal bodies, in the mutatils.
"Cult" should not be read negatively. It's probably a way to describe a proto-religion. Not as organised and consistent as modern religions, but enough similarities to indicate common worshipping practice. Certainly the most interesting part is the common culture across a large geographical area, which is quite sophisticated for the times.