Battlescript variables...

Great questions. I'm glad to see the RAM map is coming in handy.

1) From my notes, the MMMMMagic cutscene is controlled by bit 1 (0x02) of $3EBC / $1DD1. I don't think it has anything to do with $3EB9.
$3EB9 is different. The "X" is the bit index. Check out the code at C2/30E8-C2/310D for more details.
"Battle index" is just the battle number. I think FF3usME calls it the "Formation" Index.

2) The emperor's banquet thing is a little weird, and I think I remember that it doesn't really work correctly. I think it's supposed to work like this: After a battle with one of the soldiers, the screen is supposed to flash a different color depending on the outcome of the battle. Red if you died, blue if you ran out of time, green if you ran away. I didn't test this, but you can take a look at the event script at CC/886C for an example.

3) Yes, the monster variable is stored separately from the other variables. $3ED4 is the battle index and is not accessible as a battle variable.
Also, the program sets bit 7 of the monster variable when a monster uses seize. This is hardcoded into the code for seize. If you look at the AI script for the tentacle battle, it checks bit 7 of the monster variable to determine if a character has been seized.