temp solution: use 3.4.2 launcher and boot to sysnand gw mode, mount game and inject save to gw ctr there. (utilize ctrx to simplify .sav renaming)
it sucks.
Alternatively, use Cakes/Reinand temporarily to use SaveDataFiler, then go back to Gateway afterward. They can use the same emuNAND as Gateway.
You can't, GW launcher.dat 3.4.1 or even 3.6.0 won't load emunand 10.3 on N3DS (black screen).
In other words if you're on N3DS with 10.3 emunand, SaveDataFiler is broken and there's nothing that can be done about it. fuck.
Starting with Launcher.dat 3.6.1 and newer, SaveDataFiler isn't able to import save to CTR (ie: it won't create the 000400000FF40A00.sav). The remedy is to use 3.6.0, but on N3DS with 10.3 emunand, 3.6.0 isn't able to load emunand!
Hopefully they'll fix it soon; it's still working fine in the other CFWs on 10.3 N3DS though (just saying, not trying to start any CFW vs. Gateway wars here).