There's
a section in the scene.bin, at 0x0012 of the battle setup, that determines battle layouts such as "normal", "side attack" and "back attack". It may be useful to look at that section from Guard Scorpion to see whether it differs in any way from that of a battle that allows pre-emptive attacks.
There are a few other flags in the battle setup that aren't completely know yet, and it's very possible that something there may turn on or off that 16/256 possibility of getting a pre-emptive attack. I have suspicions about the escapable flag, which apparently contains other flags as well. I've noticed that most battles have FD, but most boss battles (including Guard Scorpion) have E9; a few battles that are unescapable (including the Turks in Midgar) have F9 (suggesting that there is a flag 0x40 is an escapable flag). It may be that there is also a flag here that can turn off the chance of a pre-emptive attack. (
EDIT: disregard this; it seems that F9 is more common for boss battles and that the bit I thought was for pre-emptive battles actually turns something else on/off)
BTW, have you looked at the field script from that location? Or from places where you fight boss battles that
do allow pre-emptive attacks? There may be something there that hasn't been documented yet.