Hello,
please make sure you secure your phpmyadmin install. especially zEmU seems to be a PITA [1][2]
The phpmyadmin files are stored in the apache server root only when I (rarely) must edit the database by hand, for some minutes. Otherwise, all the data is moved to a non-published filesystem. But thanks for the alert. ;)
i recommend someting like "compare db to current layout" or "compare db to xyz.initial.sql". typo3 offers this during the upgrade processes.
it's a good idea.
Regards, Viktor