Final Fantasy VI Advance Editor

Madsiur, think you mentioned you hadn't yet searched out Terra's/ Celes' Learn Lists. Terra starts at 62AAFB, and Celes follows 32 bites later at 62AB1B. The Magic Spell is listed first, followed by the level learned (so search 2D 01 00 03 32 06 for the start of the block). ...Sabin and Cyan's Ability Learn Lists are stored similarly somewhere too.

I would say the best way of making customizable learn-lists in a game is by limiting equipment as in who-can equip and then giving that equipment magic growth rates. Weapons are even better for this than relics (ex. only Relm can equip Brushes, so she can learn a personal spell from each).
This is more easily accomplished if you make certain characters learn no magic and instead give them a 2nd skill set to overwrite Magic. Example: if Cyan learns no Magic, than you can have someone else equip Katanas as well and have her learn a spell from each one.

Hacking in extra lists of natural magic is rather complicated and involves pointing from the level-up sequence (in battle and auto-leveling) to a place where there is free space and the learn lists can be created. Having this be customizable in a hacking utility would be very difficult.