This also extends to the Medallions as well. When playing the Song of Time, the game assumes that the player already has them. The game assumes these things because the player needs to have all 3 of the spiritual stones to trigger the cutscene in which they learn the Song of Time (which is also where the player obtains the Ocarina of Time). This is because the game's flags assume that, as the player knows and can play the Song of Time, then the player will have triggered the following: In order to gain access to the Master Sword, the player only needs to know the Song of Time.