In System Preferences > iCloud > Options > Documents, there are checkboxes for "Apps that store documents and data in iCloud."
For many apps, it's clear what the checkbox means: the app can, optionally, store a document in iCloud that can be accessed from any of my devices.
But there are also checkboxes for Mail, System Preferences itself, and Weather. None of those create documents. In Mail's case, the mail is stored in IMAP accounts, so what would having the checkbox checked mean? What would having the checkbox unchecked for either System Preferences or Weather mean?
In the top-level iCloud system preference, there is a separate checkbox for Mail. That checkbox, when checked, shares the configuration information for all e-mail accounts one has.