its symbolic either way. pyramids are the epicanter of there bullshit.
After Link defeated Agahnim in Hyrule Castle, Agahnim sent him to the Dark World, and deposited him on top of the pyramid. Later, after Link defeated Agahnim in Ganon's Tower, Ganon fled to the Pyramid of Power. Link destroyed him, and rescued the Triforce, which Ganon kept inside the pyramid. A lower stage of the pyramid was also home to the cursed Fat Fairy, who gives Link the Silver Arrows and the Golden Sword. It may be that the top of the Pyramid was once the spot where the Triforce shined down upon the rest of the Sacred Realm, this being due to a picture of the Sacred Realm prior to its corruption from the manual of A Link to the Past in addition to the steps that allow one to ascend to top of the pyramid from below and its location at the very heart of the Sacred Realm.