ROM Hack Integrating a mod directly into a game's patch data?

[N7Kopper]

For a while now, I've been wanting to mod Smash 3DS like I do Wii U (basic audio stuff such as fixes for Bowser and the Kongs to sound like they do in their source material, English redub packs for Marth, Cloud, Roy, and higher quality samples for the DLC characters that are already in English in the vanilla game) but it would be kind of annoying to load a patching program for a mod that doesn't change gameplay at all, as well as having to have multiple copies of the fixed audio.

So, question in the title.