Duplicate maps

Also, editing the tiles of one of these duplicate maps edits the same tiles for all of them. Unless you know how to get around that?

I think this have to do with the fact that duplicated maps use the same Tilemap (left panel of FF6LE).

Yes this definitely has to do with the tilemap, if you need another copy of a tilemap you can manipulate the settings to make a copy of a particular map. It is theoretically possible to adjust the tilemap setting to a blank one and create a new map from a newly blanked one, if there are blank tilemap ids available, which is something beyond my immediate knowledge, I've never created a map without replacing an old one.