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About this Add-on
The addon options (Tools > Addons > Advanced Unread Folders > Preferences) allow you to select folders that should always be shown, regardless of if they contain unread folders or not. By default this is set for inbox, templates and favorite folders.
If you'd only like to show special folders (like Drafts or Templates) for certain accounts, I'd suggest marking them as favorite folders and then only enabling the option to always show favorite folders.