But ... you said GBA games didn't work ... therefore you installed them in some way ...
They were form my original, non-XL 3DS. The one that I originally earned my Ambassador credentials on.
Let me see if I can explain this properly.
I first had just a bone-standard 3DS, albeit with one of the NyKo extended batteries. Not long after that, I earned the ambassador privileges, and the associated games.
When I found out about the Gateway 3DS, and the required firmware, my O3DS was already past the firmware window. At the time, my only option, was to buy another 3DS system in a vulnerable range. I lucked out and found an O3DS XL, whose sysNAND was on 4.4.
Ordered the GW 3DS almost the same day. At the time, the GW launcher was being controversial for the brick code going on. Whether by consequence or miracle, because the e-seller of the flash carts was being so slow about getting it out to me, to the point one of the fellow GBATemp mods had to go and contact them on my behalf because they flat out weren't responding to any of my own email inquiries, it arrived just in time for the newer version of said launcher to be released and available.
So, I got the GW 3DS, used the kit with my XL, and within
its emuNAND, I did the system transfer from my O3DS, to my (then-new) 3DS XL. So everything I had legitimately from then, was now on the GW emuNAND.
I never had to do a .cia for GBA or DSiWare, because I had them legit long before CFW was even a twinkle in smea's eye, let alone there being a title/package manager to allow me to install anything on either NAND.
Yes, I was disappointed that GBA and DSiWare didn't work, but there was no such thing as CFW then. And I only bothered to start looking into it when people were bragging about how CFW allowed them to actually launch those without a problem.
The rest, is proverbial history.
I hope that cleared it up. Because presently, I don't know how to word it any clearer than that.