From a user perspective I prefer it if an app as some well designed defaults and not to many settings. (Moreover every setting needs to be maintained as well). So the actual themes can be removed (personally I dont think they are are particular good looking) and just be replaced with one light and one dark theme (perhaps a third one in between is fine as well). These should be applied automatically based on the system preference.
For more advanced theming CSS is the best way, because it is highly customisable and it is obvious that CSS can break. Less tech-savvy users that want to customize Joplin can still look on the forum and c&p styles. It would be even easier if plugins could be used to apply styles, like it is possible with the macOS theme.
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