This seems like a
terrible design decision. Whatever the desired semantics, the response to a detected inconsistency between a configuration file and the filesystem should not be to
automatically and irreversibly change the filesystem.
Another WTF from that document: "It is recommended to bring the record into 'normalized' form (i.e. all objects should contain their fields sorted alphabetically by their key) before storing it there, though this is not required nor enforced."
??? Why? Will things break if I don't sort it alphabetically? If not, why recommend it? If so, why not enforce it? Nebulous half-specs like that are inevitable in systems which have evolved de-facto standards over decades, but why on Earth would you put one in a brand new spec document?
There are many other things in that document that make me scratch my head (non-user-modifiable files stored in the user's home directory?), but that's enough for one day I think...