First of all, thanks for writing a detailed explanation of your issue. What you are experiencing is bad wording of the firefox options. Indexeddb is correctly cleared, but some metadata is leftover. This metadata can not be read by the website. You can read a detailed explanation here: https://github.com/Lusito/forget-me-not/issues/175 .
Also, keep in mind, that indexeddb can not be cleared when leaving a site. Only on startup or manually. I am working with mozilla on a solution for this.