Hack with town and dungeon map edits?

You mention space limitations, but I can imagine that removing several maps would create enough space to edit existing maps, no? That way you could create a game from scratch with brand new environments. With Ember of Mana I'm working that way now, and within the limitations of it works well. Is there a way to move map data to an expanded ROM for FFVI?

Yes if you delete completely some maps it will give you space for extra tilemap data. FF6LE Rogue CE actually use a minimum of 3-4 banks of free space in expanded ROM as new tilemap space and you can even increase it to up to 6 banks iirc. It's not a complicated expansion to do iirc and other editors like FF6Tools might support it if you change the relevant code and the json definition file to point to relocated data.