It's combination of the json file and the database. Library specific settings are in the database. The profile with the custom columns names are library specific because the custom columns could be different. The list of devices is not library specific, so they will be in the json file.
The left-over options are because of a little bit of lazy programming. The options are read and then whatever is needed to be changed is changed and then saved. Nothing is clearing the old options from the in-memory copy, so they are saved as well. They won't harm anything as the code won't be looking at them. But, I'll give a little thought to a cleanup.
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