Would it be as simple as putting something in a hex editor?

What.
Anyways, the reason you need the code is because you're not supposed to be using Independent Pokemon in the first place. When you do, their results data can overwrite other parts of the game, which can lead to a corrupted save file.
So unless you know how to get around that (basically changing how the game works), you're stuck with the incredibly tedious process of having to boot Gecko to load the codes.
