At the bottom of the well…
There was nothing.
It was just ordinary stone, nothing more.
The mystical nature of the well was in the water, not the bottom of the well. As for how it refilled… Di Tou figured there was probably a formation somewhere down the well, or it was refilled periodically.
The one thing Di Tou did see was that the well was exactly a hundred kilometers and one meter.
As for why it was that long, one could say that it was an accident, but considering the nature of the architect who designed the puzzle on the hut, Di Tou felt like the final meter was simply a buffer period. Knowing that the limit of one's Spiritual Sense could never surpass a hundred kilometers, they added the final meter so that this well which could quench Spiritual Sense and allow it to extend beyond it's usual reaches would feel 'infinitely deep.'
In normal cases, it was indeed impossible to see the bottom of the well at all.