So in Legend of Zelda: Majora's Mask, you went to the land of Termina. Game Theory already proved that Termina is just Link's death world... or is it? Link dies by falling down a tree trunk in the Lost Woods. In Ocarina of Time, you can warp to different areas of the game by going through trees in the Lost Woods... see where I'm going? Link fell down the tree trunk and was transported to the land of Termina, but he was dead. He went through a ghostly journey through the land seeing new places, but familiar faces.
The land of Termina consists of 5 areas: Clock Town, The forest/swamp, The snow/mountains, The ocean, and a desert/canyon. I'm bringing up land because guess what's in Spirit Tracks? A tower in the middle, a forest, a snow area, mountains, an ocean, and a desert... These lands are pretty similar. My theory states that the land of Termina and Hyrule from Spirit Tracks are the same. Link was transported to the Spirit Tracks Hyrule via Lost Woods, however, he was transported there in (1) a different timeline and (2) 200 years before the events of Spirit Tracks, so obviously the land would have changed and Link's vision of it was based off of his memories from Hyrule.
This is all I have, but if I put more research into rather than going solely off of memory, I might have more.