I assume you do it in the tab "operations"->"optimize table"[1]. And, as an additional assumption, you do it for every table step by step?

In phpMyAdmin, once I select the database, it gives a list of all tables (Structure tab). I use the link under the list to "check all", then use the dropdown to select "optimize table".

Prior to optimization:

Results page:

If only registered users are allowed to post entries the third table stays empty.

Yes, I only allow registered users to post.