If I make a change to a model configuration setting then I don't think this change should effect every other model in the same directory.
You just hit the nail on the head. This (affecting every model in the same directory) was the intent when we developed the configuration file idea years ago. We didn't want the configuration settings to be model specific.
Having said that, yes there will be occasions where for a certain job, the configuration must be tweaked. So I agree, the present setup can lead to problems in the future if the configuration file isn't saved with the input.
Perhaps one solution would be to devise a way to "fix" the configuration items in an input file so that they won't be updated from the configuration file. We'll have to think about this ...