It can, but I'm not entirely sure how much extra saving space it allows, so it might not be possible, and it wouldn't really be useful for what OP is trying to do.
If you have digital version then there isn't much point in having a save for the O3DS payload and one for N3DS payload at the same time And you'd need to have a digital version installed to sysnand on 9.0-9.2 which might be pointless, cause if you have access to all the stuff you need to get it on there in the first place, then you probably don't need to use OoT to boot GW Launcher (although I guess it could still be useful as a second method of accessing it.)
Yeah, physical cartridges don't have enough save space in the cartridge for that unfortunately.
It -might- be possible with a digital version from the eShop, but you would need a legit copy that you actually bought from the eShop, and have a way to get it installed to your sysnand, otherwise it wouldn't be really useful.
Even then, I don't know just how much stuff the digital version can actually hold in its save file, it's possible it might not even work at all even with a digital version.
I actually have it digital on my emunand so I'll see if I can cram in lots of stuff in its save file, lol.
Edit: Yeah, even the digital version has limits to how much you can put in the save data. Oh well.
Tried putting a 903KB file lol. Maybe smaller will work idk, heh.
Anyway I just gave it a try, and digital OoT can't hold two payloads, so the idea probably wouldn't work even with digital. :/
(I'm using my retail cart dumped and converted to .cia so maybe it's a little bit different than actual eShop digital OoT? o: )
No wait, I'm able to have one save, and it lets me create a second one, just like actual eShop-bought, but attempting to create a third one crashes with the error has occurred black screen.
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.