Okay. I might have found a solution...
This actually worked for me and I was pretty surprised it did. Now, I do use CakesCFW along with Decrpyt9 instead of rxTools, so the results might be a little different I assume.
Anyways, what I did first was installed the GBA Titles on my EMUNand. I then backed up my emuNAND to emuNAND.bin and transferred that to my computer. I then backed up my SysNAND to SysNAND.bin. I then installed my SysNAND.bin onto my EmuNAND.
What I did from there was patch my EMUNand (which is now a one to one copy of my SysNAND) with the modified AGB_FIRM as well as install my GBA games on want to install on my main EMUNand (not the one to one copy of my SysNAND.)
I then put my EMUNand.bin back onto my SD Card and directly installed it on top of the EMUNand (the carbon copy of SysNAND) I patched with AGB_FIRM earlier. After that gets up and running, launch your game and is should start.
I don't know how this personally worked as they should be installed on SysNAND as well as EmuNAND normally, but it turned out fine for me. So you can try this method and see if it personally works for you.