I had forgot to change two instances of the map location data pointers. I run some new tests by changing a lot of tiles on layer 1 and 2 on a single map and the game loaded fine. Also previously, FF6LE was still writing parts of the pointers in the old location which is not the case now. I think that was the principal issue that catone pointed. I reactivated the download link with the new version.
I consider it still needs extensive testing to see if there's any other limitation with map editing.
I consider it still needs extensive testing to see if there's any other limitation with map editing.