I agree, having settings inside media portal is not the best way to go I think. HTPC's should be able simplicity and ease of use as the number one priority. Configure the system first, set-up all the imports to work automatically then release it to your family
The theory being that you don't have to do any kind of set-up once that's done unless you change your directory structure.
The only setting I can think of being any use inside the running app is a theme or icon changer.
Maybe just turn off the settings by default, or have a "superuser" account would be best, I'm sure there is a small market for people who want to do the config from the gui but maybe not the majority.