Thanks for everyone giving reports & suggestions.
By exporting GW & OoT3DHax saves (*) , we can see:
GW:
save00.bin (6KB), system.dat (34 bytes)
OoT3DHax:
save00.bin (6KB), system.dat (34 bytes), payload (43KB)
I tried renaming GW's save00.bin into save01.bin and put it together with OoT3DHax's.
However, SaveDataFiler didn't import the save01.bin in.
If manually creating a 2nd save slot in the game, black screen happened & system hanged.
If I took out the payload, then save01.bin could be imported properly.
But OoT3DHax couldn't work without payload.
So if there wasn't a smaller-sized payload, multiboot would become unavailable.
* By renaming Zelda ROM into .3DZ, MT-card can directly recognize both GW save and OoT3DHax saves, even the saves are 128KB and the header seems mismatch.
So we can use SaveDataFiler to export them.