Your file name is used to seed the random number generator, used to shuffle entrances. Every time you are spawned into the game, the mod intercepts your nextentrance id, and compares it to a master entrance id table.
The bulk of all valid entrance ids are shuffled amongst themselves, meaning that if you touch an exit that takes you into an entrance index within this list, you will only ever end up at a spawn within this list.
A much smaller subset of valid entrance ids are randomly given an id by picking a random entrance id from the master table. Entrance Ids randomized this way areable to send you to a duplicate location. For example, entry points into the «generic» and Fairy Fountain grottos are randomized in this way.
An even smaller subset of valid entrance ids are not randomized to make it possible to obtain certain items.