The preference UI can't be changed after opening settings.json in the editor

@connor thank you for the discussion :+1:

I believe you encountered the following issue where if a settings.json at any preference scope is opened while you modify values through the GUI the changes will not take effect (when auto-save is off). There is an ongoing pull-request to resolve the problem: https://github.com/eclipse-theia/theia/pull/7775.