The story is an allegory of depression
The first victim of the holes was Slender Man.
The fact that he survived to become a Humanoid Abomination led them to revise the design a few times. The one at Amigara Fault may still be a beta.The holes are a punishment on modern Japan for the mistreatment of the Ainu people
According to Owaki's dream, they were created as a punishment for terrible crimes by the people who inhabited Japan in prehistoric times. Perhaps one of their shamans had a prophetic vision, the way shamans do, that their descendants' land would be conquered by another race in the future and so they made holes shaped like the people in the vision as somekind of preemptive measure.- It wouldn't be the only time Ito has included such themes in his work—in fact, many of his stories can be read as criticism of Japanese society. The death-stench gas in Gyo was created by the Japanese military during World War II and is seemingly powered by the vengeful ghosts of people killed by Japan's wartime atrocities. Similarly, Remina is essentially a commentary on the cutthroat and exploitative nature of Japanese pop-idol culture.
Whoever created the Holes in Amigara Mountain also built the Spiral City under Kurozu-cho.
They're both enormous structures that have the power to induce unusual, self-destructive behavior in viewers. They may also be located nearby, since television broadcasts and epilogue texts from Uzumaki seem to situate Kurozu-cho in Ito's home prefecture of Gifu and Amigara Mountain is located either there or in Gunma.The holes' warping effects can be read as an allegory for the conformist nature of Japanese society.
The way the holes bend people into barely-recognizable shapes could be read as a critique of how a societal emphasis on conformity causes people to suppress the parts of themselves that don't fit, until they become unrecognisable, far removed from who they really are.