Alright! I think I found the index! I placed a Read breakpoint on the Encounter index (7E1800) started up my ready-made Zeromus event and when I did it started to CMP the value of the encounter through listings starting from 00E516 in ROM. starting with F700 which is the Dark Knight vs. Paladin battle, then continued down the list...
In RAM at...
(Note to Self: Always add +1 to hex 1B3 = 435 + 1 = Formation 436
E516 - F700 (248) - Fabul Siege Formation (Oh, I see! Rydia is never removed from the party in this event, but these formations are special so she doesn't appear.) (Edward-Yang-Cecil)
E518 - F800 (249) - Fabul Siege Formation (Edward-Yang-Cecil)
E51A - F900 (250) - Fabul Siege Formation (Edward-Yang-Cecil)
E51C - F100 (242) - Cecil vs. Kain (Cecil)
E51E - EE00 (239) - Tellah vs. Edward (Auto-Battle) (Tellah)
E520 - F600 (247) - Paladin vs. Dark Knight (Paladin Cecil)
E522 - EF00 (240) - Edward vs. WaterHag (Edward)
E524 - F000 (241) - Yang vs. 3 Imp Captains (Auto-Battle) (Yang)
E526 - F300 (244) - Tellah vs. Golbez (Auto-Battle) (Tellah)
E528 - FD00 (254) - Edge vs. Rubicant (Auto-Battle) (Edge)
E52A - A801 (425) - Adult Rydia vs. Golbez (Rydia) (UNUSED!)
E52C - 01B3 (436) - Golbez and FuSoYa vs. Zemus (Auto-Battle) (Golbez-Shadow Slot 1)
E52E - 01B4 (437) - Golbez and FuSoYa vs. Zeromus (Auto-Battle) (Golbez-Shadow Slot 1)
In ROM at...
6716 - F700 (248) - Fabul Siege Formation (Oh, I see! Rydia is never removed from the party in this event, but these formations are special so she doesn't appear.) (Edward-Yang-Cecil)
6718 - F800 (249) - Fabul Siege Formation (Edward-Yang-Cecil)
671A - F900 (250) - Fabul Siege Formation (Edward-Yang-Cecil)
671C - F100 (242) - Cecil vs. Kain (Cecil)
671E - EE00 (239) - Tellah vs. Edward (Auto-Battle) (Tellah)
6720 - F600 (247) - Paladin vs. Dark Knight (Paladin Cecil)
6722 - EF00 (240) - Edward vs. WaterHag (Edward)
6724 - F000 (241) - Yang vs. 3 Imp Captains (Auto-Battle) (Yang)
6726 - F300 (244) - Tellah vs. Golbez (Auto-Battle) (Tellah)
6728 - FD00 (254) - Edge vs. Rubicant (Auto-Battle) (Edge)
672A - A801 (425) - Adult Rydia vs. Golbez (Rydia) (UNUSED!)
672C - 01B3 (436) - Golbez and FuSoYa vs. Zemus (Auto-Battle) (Golbez-Shadow Slot 1)
672E - 01B4 (437) - Golbez and FuSoYa vs. Zeromus (Auto-Battle) (Golbez-Shadow Slot 1)
Hopefully I'll be able to find the party make-up and requirements to play the chosen formation.

I can confirm that positioning is a large part of this. I switched 01B3 and 00F1 and only Cecil appeared to fight Zemus (normal auto-battle carried out from there) 00F1 is the Cecil vs. Kain fight, which would make sense that Cecil would be alone. This means that the party is set before the formation number is found, hmm...

2: Hmm, so right above these values are values that Must correspond to "treat actor special".
E509 - 03 - Child Rydia - Hide during Fabul Fight
E50A - 03 - Child Rydia - Hide during Fabul Fight
E50B - 03 - Child Rydia - Hide during Fabul Fight
E50C - 01 - Dark Knight Cecil - Only One Present fighting Kain
E50D - 04 - Tellah 1 - Only One Present fighting Edward
E50E - 0B - Paladin Cecil - Only One Present fight Dark Knight
E50F - 05 - Edward - Only One Present fighting WaterHag
E510 - 07 - Yang 1 - Only One Present fighting Imp Captains
E511 - 0C - Tellah 3 - Only One Present fighting Golbez
E512 - 12 - Edge - Only One Present fighting Rubicante
E513 - 11 - Adult Rydia - Hide during Golbez vs. Party fight
E514 - 13 - FuSoYa - One of Two Present fighting Zemus
E515 - 15 - Golbez - One of Two Present fighting Zemus
But I've already seen first hand that it refers to the first Shadow Slot for FuSoYa's Zemus formation in particular so I have to wonder if these are even used...?

3: Phew, my money was right on the mark. They are thankfully the Only One Present or Hide commands for each special party battle, Except for the final battle's special battles. I have No idea where the game draws those, but nulling them or changing them in anyway does absolutely nothing. However the others work as you would expect change the Tellah ID of 04 to 01 to have Dark Knight Cecil beat up on Edward, for instance.
I think it's fairly clear that the normal matters are ignored for the 13 and 15, since one it's not FuSoYa it is grabbing but Shadow Slot 1 and 2, Golbez is not even in your party therefore the game should lock up when trying to access it. There is something very special going on in that particular scene, but I can't quite reason it out.
But that does solve that, looking forward to seeing Auto-battle and Special Battle's incorporated into the editor!

4: Slight addendum due to new information found below in regards to Rydia vs. Golbez.