I may be wrong here, but you could dump the cartridge rom, which would contain your save file, then use savedatafiler to extract that save then import it into the .cia installation.
If Gateway finally got rid of the fake save crypto in GW mode and uses proper encryption for >6.x games as MH4U, yes, you can (doing roughly what iViperz said). Buuuut I doubt they did so don't get your hopes up.
I don't have OoT right now so I can't test this unfortunately.