This was already mentioned in #3643, but that issue was closed without resolving the problem.
In the "Advanced Settings Editor", "Notebook", if I copy the content of "System Defaults" and paste it into "User Overrides", I get a syntax error. The reason is that the commas between the different configuration blocks are missing.
The same thing happens for "Keyboard Shortcuts"
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It seems this is not just for the notebook and keyboard shortcuts, but all settings. The individual entries of the JSON-schema are not separated by a ",", and as such the default schemas are invalid. cc @afshin