the generic patcher only replaces the URL and disable SSL, located in the main.dol
wiimmfi patcher for Mario Kart is also editing other files, like menu's text (to replace "nintendo" with "wiimmfi" text, and few other things), and also replace the match making algorythm to encouter people from all around the world more easily, instead of being stuck with "same region" random encounter.
The generic patcher work, but wiimmfi patcher has more elements/features. If you don't want to bother with the patcher, you can use the patcher option in the loader, and see if it suits you.
the loader can't patch the other files because they are not in memory at boot (and the loader is unloaded so it can't patch on the fly later when the file is loaded)