> The authors claim that modern 15th century people already knew the "pre-historic" narrative about rocks being axes.

You're mistaken, the article does not say that 15th century people knew the rock was a hand axe. The article claims (correctly I think) that the painting depicts a hand axe but doesn't say the painter intended to depict an axe. The painter would have understood the rock to be a thunderstone and painted it accurately enough that today we can see that it was actually a handaxe.