It's not something they draw attention to, but in STC the green Chaos Emerald is the Master Emerald. It's one of the six that got split in half.
It happens when they're used up. Presumably the reason it didn't happen at the end of Sonic 2 was that the final battle didn't involve Super Sonic. It also doesn't happen in-game for obvious reasons. Pretty much. Although the comic went with the Promo Comic's lore that the Grey Emerald had control over the other six. So I'm not sure what purpose the Master Emerald had in that continuity.
Although I’m team “Chaos Emeralds turned super that one time because of the master emerald” , it’s really weird that Hidden Palace in Mania has super emerald shaped stones. My conclusion is artistic freedom and it would look weird with nothing in those spots.
Nigel Kitching suggested making the grey emerald the Master Emerald in one of the scripts of the Sonic & Knuckles adaptation, but ultimately they left it green like in the game.
