Hello Everyone!
So I've been trying this. It kind of work, but not exactly as it should...
When you open a game's properties (right click -> properties), you can edit the persitent ini file (in Dolphin\Sys\GameSettings\), as well as the user ini file (in Documents\Dolphin Emulator\GameSettings\).
If you edit the first file and add your [Controls] options there, it will work. But since it's in the dolphin install directory, you'll overwrite them everytime you update dolphin.
Now with the user ini file, there is a problem. When you click 'edit configuration', the file is created and opens in your text editor, you can edit and save the file, but it's deleted as soon as you leave the games properties.