config file...
"Surely any add-ons will be registered in a config file or the registry and being open source it will be easy enough to see how that's done and do the same using a program which isn't Firefox."
Well, that's the point I think, certain people *cough*Microsoft*cough* were NOT registering in a config file, just dropping junk into the directory, so the component would execute but would not be listed for updates, compatibility checking, or uninstallation.
I assume firefox really can't control what goes into this directory (it really can't prevent anything for instance when it's not even running) but will no longer run anything that's just haphazardly dropped in there.