Gateway is not yet able to redirect/patch DS mode as I believe sysnand still handles it despite Gateway's current patches to load emunand. It must be fixed before you see DS mode (and therefor DSi/GBA mode stuff) working on emunand/Gateway mode. And unless someone comes out with CFW that outdoes what Gateway is doing, then you'll just have to wait or bite the bullet and install this to sysnand.
I might consider using this on my new 3DS XL but only after I backup my NAND before I install it. That way I can undo it. I will also create emunand before the patch is installed so as to install future fw updates to emunand without possible issues this patch may cause. Then if I do run into problems. I can just restore my NAND backup.
Perhaps a better solution is to instead create a hypervisor of sorts. Sorta like Nintendont/Devolution on a Nintendo Wii that allows booting Gamecube games without actually booting into GameCube mode. Gamecube mode doesn't really exist anymore on the WiiU, thus the reason those two programs were developed. Though I think they also work on Wii's as well and not exclusively a WiiU thing.
I don't see why the same can't be done on the 3DS. But it's going to take some major dev work to get working and perhaps more of the 3DS coding secrets need to be uncovered before we can get to that level where we can launch DS/GBA software without flipping the 3DS into DS/GBA mode. Time will tell if this becomes a reality.
EDIT:
The 3DS might not have the resources to do this perhaps, but I can definitely see this becoming a thing on the New3DS. Because DS mode games don't work once the Gateway exploit is activated, you'll have to boot off sysnand to play DS games. Therefore risk getting update prompts. Of coarse Gateway wants to be in the business of keeping their customers, so they want to avoid this.
Hopefully they won't half ass things and just create something that uninstalled the downloaded update files when you go into gateway mode again. Because that doesn't really solve the root problem of people accidentally updating the console because those accidents would occur before they can boot the exploit again. So the best thing they could do is either fix DS mode while the gateway exploit is active, or create a hypervisor similar to Nintendont/Devolution where the 3DS doesn't need DS mode anymore.
The main issue is programming. Function calls, memory addresses and all that techno-mombo are not the same when in 3DS mode thus why DS software can't boot natively while in 3DS mode. Nintendo created DS mode to handle this. I'm pretty sure it's the Arm9 that handles DS mode stuff. So code on the Arm9 side of things needs working on to get DS mode working on Gateway.
Otherwise they or another group of coders will need to create something that does DS mode without relying on Arm9 setting it up for them. They'll have to create something that can recreate the coding environment DS games expect and that's not going to be easy.
![tongue :P :P](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)