The overhead you're seeing in phpMyAdmin isn't anything to do with the MySQL settings. When records are deleted in MySQL, the space is never reclaimed until you optimize the table. Thus phpMyAdmin shows you how much space is "wasted" due to stuff that has been deleted. The user's database frequently gets stuff deleted from it, (if you are using the email verification, alot of signups never get verified and automatically deleted. The online table and search results table hold tempoary info and so they bloat quite regularly. The busier the site, the more this will happen. That's why optimizing those tables with high overhead frequently is important.
Hope that explaination helps a bit.
