If you use the GBA VC and make injects, you aren't actually emulating the GBA games, you're natively booting those games through the hardware that the DS side of the 3DS contains. As mentioned you can also opt for the open_agb_firm method which is essentially playing the games through the same method as VC and injects, though you can kinda keep them contained instead of creating titles to populate your menu as you would through the VC and injects, which may be preferential to your setup. Point is, either means isn't actually emulation for GBA games on the 3DS.