Well... Cover is cracked. It's an odd little command, admittedly with a redundant check which is quite boggling.

So how the command works is at the start of the battle the game checks to see what slot the Paladin is Occupying (thanks to the Tower of Babil docs for that bit of info.) If the Paladin is present then Cover can effectively be used.
If the Paladin is not present however or the Dark Knight Cecil is Present, Cover Cannot Work.
It's bizarre that the game would have programmed in it this safeguard that can never logically happen. In any case in RAM it is at...
0x038D61 - C9 01 (CMP with 01 ) 01 is Dark Knight Cecil's Actor Number. If the Dark Knight is Present the game will act as if the Paladin is Not.
0x038D65 - C9 0B (CMP with 0B) 0B is Paladin Cecil's Actor Number. If the Dark Knight is Present and the Paladin is, the game will still act as if the Paladin is Not.
In ROM this is at...
0x018F61 - C9 01 (CMP with 01 ) 01 is Dark Knight Cecil's Actor Number. If the Dark Knight is Present the game will act as if the Paladin is Not.
0x018F65 - C9 0B (CMP with 0B) 0B is Paladin Cecil's Actor Number. If the Dark Knight is Present and the Paladin is, the game will still act as if the Paladin is Not.
If you were giving Cover to say... Kain or Yang you would first change the 01 to an invalid number like 1F and then change 0B to their corresponding Actor Numbers. Though there is a problem you may have noticed, when a character leaves the group the next time they come back they likely are using a different Actor Number, therefore unless your game has a set party or the same instance of a character returns instead of a copy (Not sure how that would work) then Cover would no longer work. I'm sure a little more digging could be done to find why it is looking at an Actor and switch that to the Character ID, but this is fine for my purposes for the moment.

I can never just leave things be, can I? Well here's the way to change Cover's lockouts and allowances based on Character Class rather than Actor ID, making it a lot more versatile and you won't have to change things wildly to use it on a rejoining character.
In RAM at...
0x038D5C BD 00 20 - Loads what is at 7E2000 (mirrors) - This is the Actor Identifier and it's looking at this to determine if the Paladin and/or the Dark Knight is present. Changing this to BD 01 20 allows for the modder to assign the Cover functionality to a Class rather than a Character, meaning that you can freely give it to another character, no matter who they are without worry of losing it when they rejoin.
In ROM this is at...
0x018F5C BD 00 20 - Loads what is at 7E2000 (mirrors) - This is the Actor Identifier and it's looking at this to determine if the Paladin and/or the Dark Knight is present. Changing this to BD 01 20 or rather 7E2001 check, allows for the modder to assign the Cover functionality to a Class rather than a Character, meaning that you can freely give it to another character, no matter who they are without worry of losing it when they rejoin.