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Zone Doctor does all what FF6LE does plus it has other modules for hex editing, event editing, graphics, projects, data import, etc. However, Zone Doctor can easily corrupt your ROM. This is the reason why few people use it. While the level editor seem stable (the FF6LE module), the event editor on the other hand is quite buggy. This is why it is suggested to stick to hex editing for events. Zone Doctor never reached a final version, it is considered by many something to avoid for some tasks.
Madsiur made a version similar to FF6LE Rogue CE. It has the same expansion features. However since no original Zone Doctor bug were fixed, it is recommended to use FF6LE Rogue CE instead if you want to have the expansion features.