I have run into the situation numerous times (especially when working on Magento sites that were setup by other people) where configuration has been set on the website or store view levels when it didn’t need to be. You definitely cannot assume that people will always understand configuration scope.
The thing that kind of surprises me is that there is no flag/message/etc. that tells you that a setting has been set at a lower level. If you are looking at the default config, and someone has set some settings on the website level, you’ll never know unless you change the scope to the website level and find it. It would be great if there was a flag or a message next to any system config value that lets you know that settings have been set on the website/store view level. And, with multi-site instances, it should tell you which specific websites have other settings set.
I think I remember trying to create a module to do this a while back, and had a tough time figuring out how to do it well. I may take a look into it again and see if I have some better luck this time, but if anyone wants to join me in trying to figure it out – that would be awesome. It’s something the Magento community could really benefit from.