Hmm, there are some oddities. For one the Astro Tower Observatory "Underground?" is marked as YES, when it's clearly not considered underground.
Troia Castle Hospital is the same case.
It is interesting to see that the name of two of the glitch maps are "Fabul' and "Mt. Hobs East" . I wonder if maybe Fabul and Mt Hobs were supposed to originally be larger or if those labels are just placeholders?
Baron Chocobo Forest is randomly noted for having the Underground byte enabled as well.
Tower of Wishes - Final Battle has it marked, but there it makes sense since you cut to it from the Underworld/Moon.
All of the Ending maps are predictably considered underground (but now that I think on it, isn't the Astro-Observatory part of the ending?
Hmm... in the normal game is there a place called "Cave of the Lunarians"? Is that the name of the caves you enter? I don't recall that if such is the case.
Yes, it does appear that the Underground Maps are all kinds of a skewed...
It honestly seems as if it's reading the Overworld map data again. There's nothing in there that is about the Underworld. Could you give me the offsets? I'll take a look in ROM to see if the issue is with the program or the information given.

It's very clear by looking at the actual data that it does seem like the Underworld map indexes should have a special index or some such, since the labels reset back to 00/01/02, etc. Like everything else, it seems there are location labels specially for the Underworld.

2 No, that's not plausible in this case. I am a little bit certain that the editor might be misreading the proper map number? I noticed, with my own experiments that map labels are sequential... For instance... going off of Phoenix's old notes...
Tomra - 23 01 04 01 36 13 10 09 35 71 00 58 00 33
23 - Battle properties
01 - Map Index
04 - Tileset Index
01 - (Underworld) NPC Index
36 - Border Tile
13 - Map Palette Index
10 - NPC Palette Index
09 - Music Index
35 - Background Index
71 - Background Movement
00 - Appears to be load from Moon/Underworld, but that's clearly not the case since this is Tomra, an underworld map. Changing this to 80 in Tomra did absolutely nothing. None of the actual Underworld maps seem to have this byte as 80.
58 - Map Label Index (which as far as I can see the editor currently reads the Map Index for the name to display rather than the Label Index)
00 - Treasure Chest Index
I'll keep on looking to see how the game defines an Underworld Map.

3 Taking a further look into the editor's data of Village Mist and Tomra, is the editor reading the Map Index and just rereading the original data again, looking purely at the map index number to load the data? Since the data for Village Mist and Tomra are exactly the same in the editor but in ROM are...
20 01 04 01 15 04 90 09 22 71 00 28 07 - Mist
23 01 04 01 36 13 10 09 35 71 00 58 00 - Tomra
As can be seen the two are Very different in ROM.