The understanding that Koyomi was the one who put that false outlook onto the stone- how it became something bigger than it was- how it became enshrined- he was the one who put Hanekawa on that same pedestal and saw them only as someone who knows everything, someone who was a
perfect being. He was the one who put that stone there and cultivated the meaning of it and ended up with a false sense of understanding on who Hanekawa was. Once he found out who she really was, the stone loses its meaning entirely. When he finds out the stone isn't even a stone
- it's concrete. Araragi was the one who put Hanekawa onto a pedestal. The stone was concrete from the beginning. His notions were false from a beginning but he simply made himself believe it completely until he was forced to look at it directly and realize what it truly was.
The arc perfectly encapsulates Hanekawa's and Koyomi's relationship. He left Hanekawa's feelings hanging after creating a shrine around her, much like he left the shrine in a flowerbed instead of taking it home with him.
He never gave proper closure to both of them until he was forced to look at it directly.