In Twilight Princess, The Dominion Rod was used to move and navigate various non-living staues that would help you progress through the dungeon. This seems to be the overall major theme of the ToT dungeon.
My Theory states that the Ooca, the creators of the Dominion Rod, used the rod at some point, to move the ToT from it's original location to where it is in TP, Faron woods. Afterwards, they then placed the rod within the temple.
The reasons for why they would do this though, I am unsure of. Perhaps they moved it in an attempt to hide the entrance to the sacred realm.
There must have been some purpose for the creation of the Dominion rod in the first place right?
Anyways, feel free to point out any further evidense that may support this theory, or point out any flaws that may disproove it.