The only issue I see with hardcoding it to apps/USBLoaderGX/config/ is that some loaders (like the one that I am currently using) use a weird name like usbloader-gui and so I had to change my folder to that name to get the loader to work. Once there is an official loader or channel this should not be an issue but for now all of the loaders seem to use different folder names. Who really cares if you have a 'messy' SD card with a bunch of crap on it anyway? Are we really so OCD that we have to organize our SD cards?