Hi David,
I don't consider this a bug, its a feature ;-)
Module setting names are defined by the feature developer in config files and the setup page updates them accordingly so that its possible to change default settings and add new ones by updating the config file. The UI for manually entering that stuff is for developer convenience for those who have not learned to use the installation system and its config files. You should not rename module settings for existing features that you did not develop. The feature relies on those names being what they were defined as by the developer. The labels for the settings are not the same as the settings themselves, the setting name is also the resource key to lookup the label in the resource file so that labels can be localized (but not customized).
There is no reason for any user to change module setting names other than for the custom features they have developed themselves.
Best,
Joe