Everything moves between games, really. In LttP, Hyrule Castle was at the center of the map, Death Mountain to the north, Lake Hylia to the southeast, Kakariko Village to the west.
In OoT, Hyrule Castle was to the north, Death Mountain to the east of it, Kakariko Village south of Death Mountain, and Lake Hylia to the southwest.
In TP, Hyrule Castle is near the center of the map, Death Mountain is far to the east, Kakariko Village south of Death Mountain, and Lake Hylia to the southwest and much closer to the castle. (Assuming the GameCube version.)
If entire villages, landmasses, and bodies of water can move, I don't see why temples can't. The best answer I can give is, it moved because it fit the game designers' plans for how they wanted the game to flow. That's all.