Also, you might be interested in knowing that I have an unpublished script that deals with regular encounters. Allow me to re-iterate what you've already discovered (in regards to FFVI only, other PR titles may apply):
Monsters belong to Monster Party Groups
Monster Party Groups belong to Monster Set Groups
Monster Set Groups belong to Monster Dungeon Map Groups or World Map Groups
Generally, this means that there is up to 4 unique encounters per map. Something like the Floating Continent has up to 8 encounters. There is room in the data files for up to 9, but I haven't seen it used. Keep in mind that this isn't 4 unique groups per dungeon, but per map - One good example of this is in Daryl's Tomb. The first room (map) has enemies that can only be encountered in that room.
On the world map, every single tile has it's own group. While it's pretty simple and no further explanation is required beyond that, it is interesting to note that a lot of tiles are organized in a way to create "Tile Regions" (Northern Continent, Southern Continent, Thamasa) as well as "Tile Types". This is more impactful in the World of Ruin: While it's obvious Desert and Forests have different encounter sets - Did you know that the Rocky Wasteland tiles have different encounter sets from Grassy Tiles? Did you also know that, in the area around Kefka's Tower, there are 3 distinct regions with different encounter sets? Far east of Kefka's Tower, on grass, you can encounter leaf bunnies.
Anways, your on the right track and I already did it! Some things to note though: I had lots of problems getting encounters to work right. Remember how I said you can have up to 9 encounters? Well the game rolls for an encounter (steps) and then picks a random encounter (set). It's possible to pick an empty set, and the game will not force an encounter. The encounter sets are also weighted, with set 4 being a rare encounter. So there's some jank. I wanted to add some extras to the encounter script, but never got around to it. I also didn't do a write up, so this is all just off the top of my head. Oh, and I have some other scripts I was working on trying to learn.
edit: Oh, I also forgot - maybe a big important forget. Encounters outside of regular are scripted. The wandering dragons, treasure chests, bosses, etc - they have monster parties, but don't belong to a set or map. There is a few enemies that are only encounterable during these scripted events. If you miss their encounter, then you miss them forever (well ok in FFVI you might be able to force it in the veldt...). However, (and this is highly speculative) the game calls these fights by ID - it might be possible to call ANY battle from a scripted event. I wouldn't know how to do this in CE. I'm sure the script could be modified, but then at that point we are talking about modding the game. If I had to guess a valid entry point (for FFVI), it would be the coliseum - every fight there is scripted and repeatable. I just don't know how the game would handle the coliseum battle quirks. I was trying to think of enemies on the field, like where you obtain Gogo - but they aren't encounters; they just knock you off the platform. Anyways, I don't think this is something you can code across all versions of the game, but it maybe useful in an objective way at trying to understand all the different parts of the game works.
This was also a while ago, so I might be mis-remembering the issues I dealt with.
I think they all work, but yeah - there was a reason I didn't release.
. I never thought about poking into unity assets through the editor. That's genious and would have saved me so much time. I usually just navigate through the decompiled code like an idiot 
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