I guess they can edit the ROM.
http://errors.wikia.com/wiki/Pokemon_Ruby/Sapphire:_Berry_Glitch
They're older games, but it was possible at that time.
Given the fact that the GBA didn't have a "OS" that ran without a cartridge, it needed another to incert the patch.
The 3DS has a "OS", so it should be able to incert the patch by itself.
I think they eighter forgot about the gba patch, or they were lazy :/