I most likely don't have the knowledge required, but this is quite interesting. Could this be similar to what they did with FFVI on the same platform? I remember it also having a GBA rom inside. But what about the DS-only content?The rom is not inside actually. They used an 68k asm to C translator and then built around that. The rom data sections were split into resources that the game engine loads, which is why TF can be used to edit CT pc maps. The nds version also works this way, there are actually leftover reference to the DS in the PC and Android versions.
The DS content likely works the same way. One of the reasons I think why the DS content mostly consists of uninteresting fetch quests is that the original source code for the SNES version was lost, so they had to reverse engineer how the engine worked in order to implement new content.