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The current installation routine of Better Formats did not work for me on a new Drupal site. I needed to re-save the user permissions (without any alterations) to get it working.
However, those user permissions are not really _access permissions_, so it would be good to move them into a new "Display settings" tab on admin/settings/filters.
To keep it simple, just store them in a variable (i.e. no separate database table) as an associative array of roles => settings. Most probably we have to fork some code of user_access() into the retrieval function for those display settings.