Control Panels are not examined, as they execute inside the Finder. When a resource fork is opened, it is examined. If the file is infected, the open is prevented and you are told that the file is infected. Alongside all of these types of protection there is the option to log when the checks occur. Defender's log is called 'Defender Log' and stored inside the System folder.
Defender too keeps track of which Additives are around - newly discovered additives are disabled.
Warnings, bugs, etc. Thus you shouldn't fiddle with them - in particular don't change Agax's memory allocation. This will likely be improved and extended to Additives in the near future. Agax replaces Antigax and GAx Defender - you should delete these and use Agax and Defender instead. Theoretically, Agax and Defender should work from System 7.0 up.