You cannot find S3 storage option in Déjà Dup? That's because it is hidden as I found this bug report while searching for a solution.
Follow directions here to re-enable: https://wiki.gnome.org/Apps/DejaDup/Clouds
The reasons are understandable and default options are geared for casual users.
In my optinion placing advanced option under "Advanced Setting" could be sufficient.
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