Okay, i have a few things to say, it may not be about GBA specific, it is about injections. So i will proceed.
I was curious so i did some test with the cia of sonic drift 2 GG and SMB3 NES
First i tried the injector program on a GG rom, is known as Ninku 2. It has multiplayer. So i tried to inject it into a sonic drift 2 cia here is the process.
Used program to create CIA of ninku 2 rom > Used a program called 3DStool hackpack (I think by asia81) To extract the files from both Sonic Drift 2 clean cia and Ninku 2 injectec cia > Replaced the rom file in the extracted Ninku 2 cia with sonic drift 2 rom. (I simply renamed the file and deleted the original.) > Rebuild cia.
That was what i thought would be possible. It didn't work, it loaded the game but then kick you back to home menu with a error.
I tried a romhack known as Super mario bros 3 Mix. It works as a injected cia

(Good thing too) But a few others i did try didn't. Rockman 4 Minus infininty didn't work and neither did Zelda, legend of link. (I assume either the rom was too big or because of the MMC5 mapper the hacks used wasn't supported by VC) A unlicensed game (NJ063 Final fantasy VII [C!]) The program refused to inject. The files were like so.
Rockman 4 minus infinity = 1MB + MMC5 (According to the notes) Rom crashes in VC game, Grey screen, home to quit
Rockman 4 Minus infinity = 1MB + MMC3 (According to the notes) Works, didn't test long, but no problems, playable.
The rom hack is of megaman IV JAP version, and has both MMC3 and MMC5 support. I don't think there was ever offically made a published MMC5 game. Kirby's adventure, is a MMC3 game as far as i know.
Zelda Legend of Link = 2MB + Converted from MMC1 to MMC5 (According to the notes) did not work, Same as above for Rockman 4 minus infinity
Super mario bros 3 mix = Works, no known problems. Uses MMC3 (According to notes)

NJ063 - Final Fantasy VII C! = Injector refuse to accept 2 MB (No other known details)
Since Super mario bros 3 mix worked, the only thing i was curious about was the wireless play. Since is a hack of super mario bros 3 i used that cia for injection. SMB3 has wireless play, by using download play, you can download the game to another 3ds to play 2 player.
The process follows the same process above as the GG injection, but with Super mario bros 3, and the rom hack of the injected cia, but little bit more was done since i had tried to get it to work with download play.
Used hack pack to extract the CIA of SMB3 > the extracted cia has a downloadplay folder with another cia in it. (The title id is exactly identical aside from one zero having a one in place of it, might be reference to download content. "0004000
100036E00.cia") > Extracted the cia file > Replaced the rom file by renaming the rom hack inside the injected cia file the same name, and copy over. I also deleted a patch file. (I found it was causing the game not to work at first, is only found in offical VC files. So i deleted it to make the game functional) > Repacked the cia > Replaced the cia in the download play folder with the newly made one > Replace the orignial SMB rom with the romhack one. (Again, i deleted the patch file to make rom hack playable) > repackaged the rom. > Installed.
The game works, after installing the game works normally, so i tried the downloadplay. The download time was supicious for being too fast, after it was completed the screen freezes to black on the download play system. It didn't work. I compared it to the original SMB3 Cia and the download was much slower but worked normally.
So the conclusion, my idea didn't work. The gamegere replacement for wireless play didn't work and neither did the rom hack for snes replacement for download play work, and some rom hacks (weather the reason be the not supported special chips like MMC5 or the rom size being too big) didn't work. Sorry this is kinda long but i hoped some of this info help. I do appreciate the injectors, they are great.
Just in case you are curious, i provided links to each rom hack. (THEY ARE NOT ACTUAL ROMS, JUST A ARTICALE AND IPS PATCH REQUIRED TO PLAY)
Super Mario Bros. 3 Mix Rockman IV Minus Infinity Zelda Legend of Link Final Fantasy VII NES