Well, whenever I heard the name "Spirit Tracks," formulated my timeline, and figured that
ST is supposedly 100 years after
PH on the AT, I also tried to figure this out. I came up with a theory/fanfic (whichever you like to call it) that they are "spirit" tracks. Like spirits, they can move, appear, and disappear.
I've never heard of "Whistle of the Earth" but it could have something to do with commanding the tracks or controlling the earth that the tracks are on so that you can go pretty much anywhere via the train.